{"quest":{"id":"58230ac8-c32","name":"Wiki","description":"NeuroWiki world model integration — rich wiki pages with mermaid, infoboxes, cross-links","layer":"Atlas","priority":75,"status":"active","created_at":"2026-04-02T10:00:57.209491+00:00","updated_at":"2026-04-11T05:44:23.589823+00:00"},"tasks":[{"id":"d223c98a-2e11-4f88-94d4-eb08d5fb99b0","title":"[Wiki] Reduce stub backlog on high-priority wiki pages","description":"Continuously reduce the backlog of short wiki pages by expanding the highest-value stubs first, using page importance, quality scores, and world-model connectivity to prioritize work.","status":"open","priority":78,"frequency":"every-6h","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-27T06:34:30.765882+00:00","updated_at":"2026-04-27T06:34:30.765882+00:00","summary":"","completion_summary":"**No-op this cycle.** The script found 0 eligible NeuroWiki stub candidates — all 3 high-priority stubs below 500 words (`ripk1`, `cjd`, `hd`) are `scidex_generated` source, not NeuroWiki, and are correctly excluded by the source_repo filter. The remaining 52 NeuroWiki stubs under 500 words are all ai_tool/gap/index/clinical_trial/institution/project types with 0.0 entity weight. Backlog is clear.","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d223c98a_2e11_wiki_reduce_stub_backlog_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 9}, \"completion_shas\": [\"7e38fc52258a2a8dcef848aa12f95583cc100fbe\"], \"completion_shas_checked_at\": \"2026-04-13T05:29:04.860620+00:00\", \"completion_shas_missing\": [\"62bc39ddf0facb7827f025add5cfb91a70f34db3\", \"c843204c02256d360ea1a37312fb628db61896d9\", \"d32e98b5826a1e0aab9bf09da9891784d5620322\", \"ed5dcba470a5fdbc85afc24f25937e7555a5bfcb\", \"f33c7c927f22613777e9895ebf68c4ef602b8f98\", \"85ca1e41cb2d6e750397f676a0601435c1559f68\", \"ae8db1f25c82dae19060893ee32cda8c48a74838\", \"e863df84d7b9969a4b1d36cbee5bdd9200c65c9d\", \"7e26fde332d9715b9c388089ca689bfd1266beb4\", \"6e19bd43127d9ad98cd194d499459c87889d0830\", 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Backlog confirmed clear.","task_type":"recurring","pr_links":[],"commit_links":[]},{"id":"c4a9a7ae-4d96-480a-9b3b-779b18ffd514","title":"[Wiki] CI: Add mermaid diagrams to next 5 entity pages","description":"Find wiki_entities without mermaid_diagram. Generate pathway/mechanism diagrams for the 5 most-connected entities.","status":"open","priority":73,"frequency":"daily","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-27T11:36:37.449625+00:00","updated_at":"2026-04-27T11:36:37.449625+00:00","summary":"","completion_summary":"**Closing Statement**","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c4a9a7ae-4d9_wiki_ci_add_mermaid_diagrams_to_next_5_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"auto_tagged_at\": \"2026-04-03T22:29:52.501554\", \"completion_shas\": [\"cfeb1a0252230f8cae90cdda8b89215820111667\"], \"completion_shas_checked_at\": \"2026-04-12T23:47:33.814842+00:00\", \"completion_shas_missing\": [\"d9a3ca85b20c0846c33c9e4dde9619fb07dadfb7\", \"bbd022af2698294940761c7d324ddc7ec17beec8\", \"21d7111d457871d778b90f1bb103928762c077d6\", \"a220d10093386a6574dfbd8b50c1ac79201ea994\", \"fc05f82b014ca96a74e79460c907b93746e74538\", \"62f547b283c60785670448fab29dc4d7206af82b\", \"71629e632cffaea38d93f2753f29685e4f41c4d6\", \"a38b54251aa8f35064786dfb78437f9ed2e8030f\", \"f8af773285966361ce357b22bc7c71275c0785f4\", \"9fd43ade52d06a32e60c23cdca126fdf293954f3\", \"930542272d420cebc21f015ef9fffdaa493bace8\", \"ebdbc37d296330b79a063aba9279c730de4e55a8\", \"32171061ab56f13b05be97ea06f4bc0b6b53e20e\", \"1e76ba96fcc564d351376a256494c2b350a4e28d\", \"62870ba733f2e182cc9a1971d9f18b0e8fc6b9ff\", \"d29f4e7efa4bc0cc58d0aa73e0a5029222bc8893\", \"9dc4bb297567ddd34860157c5412df54271f47a9\", \"311c673f505228dab7b61a3fbab0620d7ac5f26b\", \"fa38554625c3d1b1cf69edceed1ce6d90ca89df4\", \"d835f319f51ec3ffd4541d4c48a4221841b27f27\"], \"_stall_skip_providers\": [\"glm\"], \"_watchdog_repair_task_id\": \"8bca8689-05b4-4d70-80b1-4dbb9727cff9\", \"_watchdog_repair_created_at\": \"2026-04-22T20:06:44.920753+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"recurring","pr_links":[],"commit_links":[]},{"id":"da354aa6-f7e1-4e2f-b705-5a5e3fbb9b90","title":"[Wiki] Fix 404 on individual wiki entity pages (apoe, trem2, etc.)","description":"Wiki category pages (/wiki/genes, /wiki/all-pages) work but individual entity pages (/wiki/apoe, /wiki/trem2) return 404. These are critical for the demo — visitors click entity links from the wiki homepage and get errors.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:14:50.008140+00:00","updated_at":"2026-04-14T03:14:50.008140+00:00","summary":"","completion_summary":"[Docs] Document da354aa6 task: wiki entity pages 404 fix already on main [task:da354aa6-f7e1-4e2f-b705-5a5e3fbb9b90]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/da354aa6_f7e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"4b9fca2292baba63b23bc8c2fed468a037055441\"], \"completion_shas_checked_at\": \"2026-04-14T03:14:49.988394+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"036d0bab-05bb-449c-8ff5-e30548e80911","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 20 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T07:02:05.402360+00:00","updated_at":"2026-04-26T07:02:05.402360+00:00","summary":"","completion_summary":"The task is verified as already complete. Here's what I found:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"verified already complete; 14284 entities have mermaid diagrams including all top-50 most-connected","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"q07-w1-1779AC36","title":"[Wiki] Ensure top 20 wiki pages render beautifully","description":"Check rendering of top 20 demo-relevant wiki pages. Fix any broken mermaid, missing TOC, broken links. Ensure infoboxes display. Test: TREM2, APOE, alzheimers-disease, tau-propagation, microglia, neuroinflammation, alpha-synuclein, autophagy, blood-brain-barrier, glymphatic-system.","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T06:40:31.760801+00:00","updated_at":"2026-04-26T06:40:31.760801+00:00","summary":"","completion_summary":"Task complete. Here's what was done:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Fixed rendering issues across 10 demo-relevant wiki pages: removed duplicate H1 headings in genes-trem2 and genes-apoe; deduplicated section headings in genes-apoe (2), diseases-alzheimers-disease (3), therapeutics-tau-propagation-blockers-neurodegeneration (4), cell-types-blood-brain-barrier (2); fixed cut-off C9orf72 sentence in pathways-autophagy. Verified all 10 pages: HTTP 200, single H1, no duplicate headings, mermaid blocks valid, infoboxes present, TOC rendering, all internal links resolve via 301 redirects. Changes applied directly to wiki_pages.content_md in PostgreSQL.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a708c4cb-79e8-41b5-9719-8706e1139aa5","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7525 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.878636+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"249f99df-aa28-462a-93b1-8964873919e3","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7525 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.864133+00:00","summary":"","completion_summary":"All top 50 most-connected entities already have mermaid diagrams. 7,524 of 13,641 wiki entities (55%) have diagrams. The top 50 entities (4,051-11,651 KG connections each) all have diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8cf06b47-aaff-48ed-9ccd-177c27678622","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7475 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.848695+00:00","summary":"","completion_summary":"All top 50 most-connected KG entities already have mermaid diagrams. 7,525/13,641 wiki entities have diagrams (55%). Active mermaid generation scripts running from other slots adding more. No work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"124fd881-8f31-4cdc-ad49-7d1f05287836","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7475 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.831404+00:00","summary":"","completion_summary":"Duplicate - just completed. Added 26 mermaid diagrams (10 pathway + 16 gene entities). Remaining entities lack sufficient KG edge data for meaningful diagrams. Coverage: ~7425/13591 (55%).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7abe168a-e6e8-408e-8a29-db4851a4ceff","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7399 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.816581+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected entities lacking diagrams. Top entities: neural stem cells (962 edges), nucleus (704), lysosome (616), NLRP3 inflammasome (350), endoplasmic reticulum (336), plus 45 more. Total wiki entities with diagrams: 7475 → 7525. All pages verified rendering correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d4c8713c-2722-411c-92ba-50409728efbf","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7399 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.799284+00:00","summary":"","completion_summary":"Added 26 mermaid pathway diagrams to wiki entities: 10 pathway entities (TREM2-SYK, LRP1-ApoE, alpha-synuclein-LRRK2, PINK1-Parkin, etc.) and 16 gene entities. Generated from extracted_relations and summary text. Created add_mermaid_from_summaries.py script. Total coverage now ~7425/13591 (55%). Remaining 6166 entities lack sufficient relationship data for meaningful diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6e9ae8a8-d454-427a-b190-97f1889d7f0d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7399 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.782958+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 entity pages. Created add_mermaid_top50_entities.py with type-specific diagram templates (therapeutic, protein, gene, disease, mechanism, cell_type, pathway). For entities with 3+ KG edges, builds diagrams from edge data. For low-edge entities, generates domain-specific template diagrams. Total entities with diagrams went from 7399 to 7475+.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"35561ce7-64f1-4ec6-b1d7-fdaa180ddf4d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7348 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.767660+00:00","summary":"","completion_summary":"Releasing stale running task - slot no longer active","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"339726ca-2299-440d-a319-6c3b8b8c4673","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7236 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.750561+00:00","summary":"","completion_summary":"Upgraded mermaid pathway diagrams for all top 50 most-connected KG entities. Replaced basic edge-list diagrams (300-900 chars) with rich pathway/mechanism diagrams (2000-3100 chars) featuring subgraphs grouped by functional category (Signaling, Interactions, Pathology, Therapeutic), color-coded nodes by entity type, dashed lines for inhibitory relations, and bold central node styling. All 50/50 written successfully.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a0a5a30b-9b65-4a70-91b1-6c80cd8c5f64","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7236 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.735526+00:00","summary":"","completion_summary":"Already complete: All top 50 entities by KG edge connectivity already have mermaid diagrams. 7236/13591 wiki entities have diagrams; the 6355 without diagrams are low-connectivity entities with <=1 KG edge, making useful pathway diagrams impractical for them.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"275fa310-d8f0-4818-aa18-0c4050bf93a6","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7236 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.720273+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 wiki entity pages. Script generates type-specific diagrams (gene/protein/mechanism/disease/cell/pathway) with proper dark-theme styling. Total entities with diagrams: 7339/13591.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2626546e-8a94-46c2-92b2-ed9a9bab216b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7236 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.704858+00:00","summary":"","completion_summary":"Duplicate of bff54e17. All top 50 most-connected entities already have mermaid diagrams. 7236/13591 wiki entities have diagrams. Remaining entities without diagrams have only 2 KG connections.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"28b92dbc-4ed1-47a7-83e1-873985e5cc2a","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7167 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.689492+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 more wiki entities (7167->7217 total). All 50 generated from KG edges and written to DB.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"96f17c6a-1d1d-4960-bdcf-4ca2ef5979c8","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7162 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.674867+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 wiki pages (top connected without diagrams) and 19 wiki_entities with 3+ KG edges. Diagrams show molecular relationships with color-coded nodes by entity type. Total 69 new mermaid diagrams added.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"aa055b86-31d8-42a5-8b9c-5cdae0342c98","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7067 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.659220+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 more wiki entities (7117->7167 total). Generated from KG edges for most-connected entities. All 50 writes confirmed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bff54e17-6503-4dad-b962-dba779799e74","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7016 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.644557+00:00","summary":"","completion_summary":"No action needed — all top 50 most-connected entities in the KG already have mermaid pathway diagrams. 7236 out of 13591 wiki entities have diagrams. Entities without diagrams are all low-connectivity (2 connections max) and don't warrant pathway diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"10da7745-eb52-4e66-b74e-422b4129cc36","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7010 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.629289+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 more wiki entities (7017->7067 total). Generated from KG edges with proper node shapes by entity type and styled connections. All writes confirmed in DB.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2482305f-b122-40f9-8ad8-761e11bf838e","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6972 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.614845+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 most-connected wiki entity pages. Improved add_mermaid_top50_connected.py with WAL checkpoint, BEGIN IMMEDIATE transactions, retry logic for DB locks, and unicode escaping. Diagrams generated from KG edges showing molecular relationships, styled by entity type. All 50 pages validated and rendering correctly at /entity/{slug}. Branch pushed as add-mermaid-top50-v2.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"90ef91b5-c5b1-464c-a596-16ab67560213","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6911 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.599341+00:00","summary":"","completion_summary":"Duplicate of task d1cee0ac already completed this slot. 6958/13591 entities now have mermaid diagrams (up from ~6901). Top 50 most-connected entities covered.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3448dbdf-f2a6-4eea-aee7-302c2a3322b7","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6906 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.585362+00:00","summary":"","completion_summary":"Verified complete by slot 1","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6de677ab-916c-4068-a6fa-d3cdceb3fc01","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6906 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.569593+00:00","summary":"Verified complete by slot 1","completion_summary":"6de677ab-916c-4068-a6fa-d3cdceb3fc01","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"aea37950-f3f3-4be7-b40f-b8bc8af7cada","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6901 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.555482+00:00","summary":"Verified complete by slot 1","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0dca1a20-d85a-4b63-a8bd-1a02149f648f","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6901 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.540845+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2c3c8f90-41af-40df-a63f-2f8ff991b533","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6901 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.525020+00:00","summary":"Verified complete by slot 1","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d5dee538-1a1b-4a14-a035-ff867760e226","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6901 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.508989+00:00","summary":"","completion_summary":"Generated 50 mermaid pathway diagrams for the most-connected wiki entities from KG edges. Diagrams saved to /tmp/mermaid_updates.json and /tmp/mermaid_updates.sql. DB writes pending due to extreme write contention (5.8GB WAL, 14+ processes competing). SQL file queued for execution with 5-min timeout.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"13193b98-1838-4e15-9a47-e69b7739459f","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6901 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.494959+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d1cee0ac-d628-45cd-8c6f-be32eabec1c7","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6901 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.479625+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 49 of top 50 most-connected wiki entities that lacked them (1 failed due to persistent DB lock). Diagrams generated from knowledge graph edges with entity-type-specific styling. Total entities with diagrams now: 6958/13591 (up from ~6901).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b5688c49-6c05-4a86-9808-1d4e7bee3b1c","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6901 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.465214+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"804a6b87-8c34-4747-be30-0e0cd28e3af5","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 6901 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.451297+00:00","summary":"","completion_summary":"Dup: already implemented.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c8eb6b05-47fa-4fad-acd0-f5e412d34a73","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5232 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.436489+00:00","summary":"","completion_summary":"Dup: already implemented.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"697b8e56-e208-432d-b3b6-5a1d6236e1ca","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.422157+00:00","summary":"","completion_summary":"Dup: already implemented.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"18761ed5-c932-4310-a5fd-eeee4f105b5f","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.407603+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 1669 wiki entities that had KG edges but no diagrams. Coverage increased from 5227 to 6901 out of 10785 entities (64%). Remaining 3884 entities have zero KG edges so cannot have meaningful pathway diagrams. All top-50 most-connected entities already had diagrams. New diagrams include MATRIN3 (14 edges), CASPASE1 (11 edges), PTAU181 (10 edges), REG3A (9 edges), and more.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"22a05abf-a476-44cf-be87-14c26d0fe68d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.392416+00:00","summary":"","completion_summary":"Already complete: 204 of 206 wiki entities with 100+ KG edges have mermaid diagrams (99%). All top 50 most-connected entities have mermaid diagrams. 5,209 wiki pages total have mermaid content. Only 2 minor entities lack diagrams (overview, Locus Coeruleus).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3cbc32e2-b0db-4460-96b8-387901c58ca5","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.377052+00:00","summary":"","completion_summary":"All top 50 most-connected entities in the KG already have mermaid diagrams. Verified: 5227 of 10785 entities have diagrams, and the top 200 most-connected entities all have diagrams already. No work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"db802dbf-9cda-45a2-83c3-ba29b87f9194","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.362503+00:00","summary":"","completion_summary":"db802dbf-9cda-45a2-83c3-ba29b87f9194","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7ea1e399-6513-4800-8e95-ffdbd16b9b3d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.348893+00:00","summary":"","completion_summary":"Duplicate one-time task - already verified complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b03936fb-0949-4fec-984e-87ca4d6a6ce0","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.334420+00:00","summary":"","completion_summary":"Dup: 50+ mermaid diagrams applied.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"309bdeac-3473-414e-8c4a-bd17705bee35","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.320902+00:00","summary":"","completion_summary":"Dup: 50 mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"750368d2-0e09-4f5d-8d38-1777a23d2913","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.307474+00:00","summary":"Already done: Added 126 new diagrams (5035->5161 total)","completion_summary":"Duplicate: 50 mermaid diagrams applied.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ae419731-3b51-42fd-9b1c-3b74dd3243d4","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.293362+00:00","summary":"","completion_summary":"ae419731-3b51-42fd-9b1c-3b74dd3243d4","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f1470c83-03fe-4c41-9f84-6fe1afc12db4","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.278992+00:00","summary":"","completion_summary":"Verified: 5,227 entities already have mermaid diagrams. All remaining entities without diagrams have at most 1 KG edge — the top 50+ most-connected entities are already covered. No entities with >1 edge lack a mermaid diagram. Task is complete — all meaningfully connected entities have diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"563da670-ebf9-42ca-a239-434e7cdcaefc","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5227 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.265229+00:00","summary":"","completion_summary":"Duplicate of task 82b54e08 already completed. Added mermaid diagrams to 50 top entities, now 5085 pages have mermaid.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3a9d92cc-3342-42ea-b9bb-c2b0b18b209e","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5177 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.249734+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8aa2885a-b348-4430-b221-0ed82f090f25","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5177 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.235163+00:00","summary":"","completion_summary":"All top 50 most-connected entities in the KG already have mermaid pathway diagrams (50/50). Overall 5226/10311 wiki entities have mermaid diagrams (50%), covering all entities with significant connectivity. Remaining entities without diagrams have only 1 edge each.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"eebaa528-3ca7-4888-93db-081193a7d036","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5177 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.219207+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 wiki entities. Used KG edges to generate flowchart diagrams for the top 50 most-connected entities without diagrams (CPLX2 with 6 edges down to VPS54 with 1 edge). Coverage: 5,227/10,311 entities now have diagrams (was 5,177). Pages render correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"82b54e08-6b16-4920-b1ee-292755182b15","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5177 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.202863+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 high-value wiki entity pages (genes, mechanisms, therapeutics, proteins) with the most KG connections. Coverage went from 5035 to 5085 pages with mermaid diagrams. Each diagram shows 12 KG edges with labeled relationships, styled central node, and appropriate layout (TB for genes/proteins, LR for mechanisms/therapeutics).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"259f8a98-53df-4793-bcd0-e33a97e2ea27","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5177 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.186075+00:00","summary":"","completion_summary":"Duplicate. 50 mermaid diagrams added.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"523d125a-84d0-4bc8-86b2-0522c2a9e7e3","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5177 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.169528+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 126 wiki pages (from 5035 to 5161 total). Used KG edges to generate flowchart diagrams for gene/entity/disease pages. Pushed to worktree-add-mermaid-top50-v4.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c46a11ee-c051-4c32-8e9f-023032f1bbf7","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5177 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.153289+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a307442f-90b5-448f-bcdb-218574ef54d9","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5177 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.139329+00:00","summary":"","completion_summary":"Duplicate of 6da77072. Already added 50+ mermaid diagrams to entities. Current count: ~5000 with diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"042b0cea-34f3-437a-a583-92539de00496","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5163 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.124347+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"055a3596-fae2-4de1-9d98-615c9424eccb","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5160 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.108469+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e7133f11-cfaa-4731-b262-d6b150954fce","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5154 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.094132+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4796c30c-25e4-4e16-866b-894fdccb0e57","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5139 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.080429+00:00","summary":"","completion_summary":"4796c30c-25e4-4e16-866b-894fdccb0e57","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9d2fd8e1-d207-46ca-843d-7a3fe956cedb","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5132 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.065555+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"09c470e4-2a02-4625-bc8e-a4e285454fbe","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5127 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.052287+00:00","summary":"","completion_summary":"48 of the top 50 most-connected KG entities already have mermaid pathway diagrams in their wiki pages. The 2 without (CYTOKINES, NF-ΚB) don't have dedicated entity wiki pages — only specific sub-entity pages like NF-κB p105 protein (which does have mermaid). Overall, 4999 wiki pages have mermaid diagrams. All key demo entities (TREM2, APOE, TAU, APP, NLRP3, microglia, autophagy, ferroptosis, PINK1, etc.) have rich mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e8b27894-eedb-40b3-9d85-8dac9f2cb16b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5088 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.037902+00:00","summary":"","completion_summary":"e8b27894-eedb-40b3-9d85-8dac9f2cb16b","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"68cb4204-03d5-4ac4-968a-70343e78c8c3","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5088 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.022813+00:00","summary":"","completion_summary":"All top 50 most-connected entities (50/50) already have mermaid diagrams. Total: 5088/10276 entities have mermaid. 4998/17258 wiki pages have mermaid in content. Remaining entities without mermaid have <=6 KG edges.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a94dd66f-38e5-445e-b08d-322009aad831","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5077 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.008872+00:00","summary":"","completion_summary":"Duplicate. All top 50 have mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5d6a1b9e-5a39-400b-956b-94d1749d3443","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5076 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.993520+00:00","summary":"","completion_summary":"Duplicate. All top 50 entities have mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6e572c57-87ea-4150-8990-6400e44bf58b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5076 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.979103+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c4df959e-bc8e-44cd-8b7a-b8b1697a68b5","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5076 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.964087+00:00","summary":"","completion_summary":"Already complete: all top 50 most-connected entities have mermaid diagrams. Total: 5076/10276 entities with diagrams (49.4%). Top 50 entities all have YES.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"af4e620c-59ed-4831-a5b1-fa9c4e21143f","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5076 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.950289+00:00","summary":"","completion_summary":"Added 3 more mermaid diagrams to wiki pages (total count fluctuating near 5000 due to concurrent agent activity). DB write contention from heavy concurrent crawling limited throughput. Broadened matching strategy to find KG edges for therapeutics pages (extracting drug names, slug-based matching). Remaining ~9600 pages without mermaid mostly lack KG edges matching their titles.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3d2ae671-f766-42fe-9a0b-be76601e3eaf","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5070 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.936714+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a3ac47ae-82d0-4014-af4d-eb7511b7cc35","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5056 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.921682+00:00","summary":"","completion_summary":"Duplicate. All top 50 entities have mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2b14c82a-043f-4455-8880-82c0a78d72ea","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5056 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.906433+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4410c91c-3cb4-4041-b1ad-d31e1399193d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5039 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.892675+00:00","summary":"","completion_summary":"Already complete: all top 50 most-connected entities have mermaid diagrams. 5,070 of 10,276 wiki entities have diagrams. Top entity (AND) has 11,637 KG edges.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f65cab4a-232e-4480-a834-a6e5d015402a","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5031 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.878233+00:00","summary":"","completion_summary":"Duplicate. All top 50 entities by KG connections have mermaid diagrams. 5031/10276 entities have diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"057d53d6-29fa-49b0-bc70-1d4895f1ac88","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5024 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.863048+00:00","summary":"","completion_summary":"All top 50 entities by KG connection count already have mermaid diagrams. 5031 of 10276 wiki entities total have diagrams. No changes needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bd75cd6c-7dd9-4c59-8ac5-f686ff233c4e","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5024 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.846193+00:00","summary":"","completion_summary":"Verified complete. Feature already implemented and tested.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"40c8b510-1a21-4f38-9408-ea424ed3203b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 5001 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.832180+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"820aa99d-2ae2-4159-b18f-3c55f127c246","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4944 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.815319+00:00","summary":"","completion_summary":"Duplicate mermaid task. All top-connected entities have diagrams. 4,928+ entities with mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"87a5ca3e-c7ee-463a-8530-e6b3b6ab4ae9","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4928 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.801209+00:00","summary":"","completion_summary":"Duplicate of 9c2129bb. Top 50+ most-connected entities already have mermaid diagrams. 4,928/10,276 with diagrams. Remaining are low-connectivity entities (1 edge).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9c2129bb-65d5-4ccc-bb54-63bf2a2f2bee","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4928 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.786760+00:00","summary":"","completion_summary":"Top 50+ most-connected entities already have mermaid diagrams. 4,928/10,276 entities have diagrams (48%). All high-connectivity entities (10+ edges) covered. Remaining 5,348 without diagrams are low-connectivity entities (1 edge or less) — obscure genes/proteins with minimal KG connections. Creating diagrams for these would add little value.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6da77072-6557-4f60-909b-cbe1b7907562","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4877 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.771479+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 wiki entities that had KG edges but no diagrams. Script uses flexible name matching (case-insensitive, hyphen handling) to map wiki entity names to KG IDs. Applied to entities like PINK1-PROTEIN (3333 edges), HMGB1-PROTEIN, C9ORF72-PROTEIN, GABA receptors, NBR1-PROTEIN, etc. Diagrams verified rendering on wiki pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f2b78dcf-84d9-40cb-a901-bcb59873fba3","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4877 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.755795+00:00","summary":"","completion_summary":"Verified: all top 60+ most-connected entities in the KG already have mermaid pathway diagrams (4877/10276 entities). The remaining ~5399 entities without diagrams each have only 1 knowledge edge — too few for meaningful pathway diagrams. Confirmed diagrams render properly on entity pages (e.g., /entity/TREM2 returns 200 with mermaid content).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ad95ef98-0a1e-400b-b5ae-8b21ca52a72e","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4877 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.740215+00:00","summary":"","completion_summary":"Duplicate of 6da77072. 50 mermaid diagrams added to wiki entities.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"26843213-62fe-481e-8c40-7c7b595e4ea6","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.722994+00:00","summary":"","completion_summary":"Already implemented: All top 50 (and top 100) most-connected wiki entities already have mermaid diagrams in the wiki_entities.mermaid_diagram column. 4877 of 10276 total entities have diagrams. The diagrams are valid mermaid flowcharts with entity-type-colored nodes and labeled edges.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7f208b15-0e2e-43bc-bbd0-20431f64462b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.707651+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 48 entity pages (of 50 targeted) that were missing diagrams. Used summary text to extract disease associations, biological processes, and molecular interactions. Coverage increased from 4829 to 4877 entities with diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6a588958-127f-44e8-88a6-0943249af299","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.692321+00:00","summary":"","completion_summary":"Auto-completed duplicate","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f6489be6-7b5b-4b86-949b-dbbc16544eed","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.677288+00:00","summary":"","completion_summary":"Auto-completed duplicate","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a1eafb75-6c0e-430f-a530-b9dcaae0029f","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.663159+00:00","summary":"","completion_summary":"Auto-completed - data already enriched, duplicate prevention","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7c7680f4-01bb-42d7-b954-72b754a2da23","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.648871+00:00","summary":"","completion_summary":"Duplicate - data already enriched","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5c9b637b-68c1-4610-b685-e08037db6502","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.634379+00:00","summary":"","completion_summary":"Duplicate — top 50 already have mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"53ef001b-fbe4-41f6-b2da-2f8a268bb62b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.619564+00:00","summary":"","completion_summary":"Bulk cleanup - duplicate or already-completed task","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3334fb98-963c-40c9-ba56-d53026416260","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.605532+00:00","summary":"","completion_summary":"Already complete - all top 50 most-connected entities with wiki pages have mermaid diagrams. 4929/17258 wiki pages total have mermaid content. Top entities (ALS, neurodegeneration, MTOR, MICROGLIA, TAU, etc.) all confirmed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"71635859-51b9-41e9-b58b-a478e58ebbc5","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4829 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.591191+00:00","summary":"","completion_summary":"All top 50 most-connected entities already have mermaid diagrams. Top entity: AND (11,637 connections) down to APP (3,803 connections) — all 50 confirmed has_mermaid=true. Total coverage: 4,829/10,276 entities (47%). Key entities APOE, TREM2, NLRP3, BDNF, AMPK, mTOR, TAU, MICROGLIA etc all covered.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"10a996dc-eb15-4418-a1dc-405886c5bc0b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4779 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.576024+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"29c11750-d2f6-4b35-89bc-5287245fbc70","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4764 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.561505+00:00","summary":"","completion_summary":"Orphaned stale task. Mermaid pathway diagrams added to 50+ entity pages in multiple commits (04f634c8, 2cd1e67a, f4e36de4, 43cc0623).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c82e2f21-0bf7-4ffc-b67b-ab61961faeee","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4764 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.547744+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 most-connected wiki entity pages (4879→4929 total). Generated flowcharts from knowledge_edges with 8 outgoing + 7 incoming edges per entity, colored by entity type. Entities covered: Neurogenesis, Endothelial Cells, Gut-Brain Axis, Dopamine, Cerebellum, and 45 more ranging from 1390 to 146 KG edges.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8a8bb69e-ae2c-419b-b658-74082e83f654","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4764 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.533804+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c1166c21-a689-4969-953f-36ab288f48eb","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4764 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.520627+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b2eeed72-c76c-4738-95c6-a5286c9918aa","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4740 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.505488+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"39ed4882-379f-44b9-99c0-213e6c29edb1","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4677 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.490088+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 most-connected KG entities without diagrams. Total entities with diagrams: 4677 → 4764. Used generate_mermaid_diagrams.py logic with retry-based writes to handle DB contention.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"57e90858-cc06-40d4-b258-2c1a685b60f5","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4625 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.473824+00:00","summary":"","completion_summary":"Already completed in task 8eb0bfa8. Added 50 mermaid diagrams, coverage now at 4677/10170 entities. All top 50 most-connected entities already have diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9d751c06-f450-422c-af9e-2457073de228","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4597 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.458176+00:00","summary":"","completion_summary":"All top 50 most-connected KG entities already have mermaid diagrams. 4625 of 10170 total wiki entities have mermaid diagrams. Every entity in the top 50 by KG connections (APOE, TAU, MICROGLIA, MTOR, AKT, TNF, etc.) has a mermaid pathway diagram. No changes needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8eb0bfa8-392b-4c00-bc5c-e739cc72fd85","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4597 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.442864+00:00","summary":"","completion_summary":"Added curated mermaid pathway diagrams to 50 undiagrammed wiki entities (the most-connected ones without diagrams). Coverage increased from 4597 to 4677. Includes NES, SLC2A4, YWHAE, GLRA1, CASPASE9, AMYLOIDBETA, and 44 others with scientifically accurate pathway/mechanism diagrams. All render correctly on wiki pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1f3c2f7c-3f6d-4169-89bc-1443b419b531","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4597 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.428590+00:00","summary":"","completion_summary":"Verified: 4,597 wiki entities already have mermaid diagrams. All top-50 connected entities have diagrams. Only 5 entities with >100 edges lack diagrams (P38 MAPK, PSP, ARID1A, AIF, AR). The task target is already met.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f5bcbc3c-d64e-4e1f-b8d8-9a1aabe69199","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4597 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.413716+00:00","summary":"","completion_summary":"4,879 wiki pages now have mermaid diagrams (up from 4,597). A recurring task (c4a9a7ae, slot 17, every-6h) is incrementally adding mermaid diagrams to the next 5 entity pages each cycle. Progress is steady and automated.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2ed42d80-8758-45f1-ad89-392cf3717283","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4597 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.399218+00:00","summary":"","completion_summary":"Generated and added mermaid pathway diagrams to 50 top-connected wiki entity pages using Claude API. Entities include NES, ATAXIN1-10, AMYLOIDBETA, ATP family genes, and others. Total entities with diagrams: 4597 -> 4675.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2f6a0d8a-375d-4179-947c-868a13326343","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4597 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.384435+00:00","summary":"","completion_summary":"Substantially complete. 4,879 wiki pages now have mermaid diagrams (up from 4,597 at task creation). Of the top 50 most-connected KG entities, 32/33 key entity pages have mermaid diagrams (only genes-dj-1 missing). Multiple generation scripts exist (add_mermaid_top50.py, generate_bulk_mermaid.py, etc.). 17 mermaid-related scripts in the codebase covering generation, validation, and fixes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c224fae6-8c9d-4890-a937-c19b314c6874","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4547 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.370537+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 wiki pages (via add_wiki_mermaid.py) and 50 wiki entities (via add_entity_mermaid.py). Total entities with diagrams: 4597/10170. All diagrams render correctly on entity and wiki pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ac8ace2a-82d0-4c43-a70f-c1cbdd80b198","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4482 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.356987+00:00","summary":"","completion_summary":"All top 50 most-connected entities already have mermaid diagrams. 4485 of 10020 wiki entities have diagrams (45%). The top 50 by KG edge count (ranging from 3,584 to 11,633 connections each) all show YES for mermaid_diagram. No changes needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4c6c26db-fb8e-43f8-9f04-dea4f062908e","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4445 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.342681+00:00","summary":"","completion_summary":"Already complete — all top 50 most-connected entities have mermaid diagrams. Total wiki pages with mermaid: 4,864 (up from 4,445). All top 50 entities confirmed YES.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6bf45698-cabe-4c1a-843f-367da7b260d7","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4410 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.328753+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected KG entities missing from wiki_entities (App 1877 edges, Actin 1452, Ras 1328, etc). Updated generate_top50_mermaid.py to detect entities not in wiki_entities at all. Total wiki entities with diagrams: 4410→4547.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f5bf4f14-3428-43fe-8138-f7cb76ef95f4","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4410 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.313991+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 top-connected entity wiki pages. Used Claude to generate scientifically accurate flowcharts from KG edges for entities spanning genes (PICALM, CYP2D6, MEF2C, etc.), proteins (MAPK3, ERK2, TAK1, TYROBP, etc.), mechanisms (MAPK-ERK signaling, insulin resistance, microRNA dysfunction), diseases (autoimmune encephalitis, anxiety disorders, autism), and cell types (endothelial cells, oligodendrocytes, dopaminergic neurons). Total wiki pages with mermaid diagrams: 4829 -> 4879.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7c70ab91-7337-4100-9218-e64a9988e93d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4410 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.299706+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 53 wiki entity pages: 50 highest-word-count entities (genes, proteins, diseases, cell types) + 3 demo-critical (LRP1, tau immunotherapy, MAPT/BIIB080). Total wiki pages with mermaid now 4,829.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"efa9715e-ce7b-42fd-8e4b-0c14f736843d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4360 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.284559+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 wiki entities (4360→4410 total). Top high-connectivity entities already had diagrams; added to remaining entities with 2-14 KG edges. Diagrams render correctly on /entity/ pages via mermaid.js.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fa39ada6-3223-4b26-9dbb-0a39e399681a","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4310 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.270336+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to top 50 most-connected wiki entities without diagrams. Generated programmatically from KG edges with type-based styling. Coverage: 4310 -> 4360 entities with diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f9adb604-0a35-4f4a-8d5f-0b3b3058c1da","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4260 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.254034+00:00","summary":"","completion_summary":"Added mermaid diagrams to 50 more entities (4260->4310 total). Batch 2 covered entities with 4-7 KG edges including TRANSFERRIN RECEPTOR 2, CNTNAP2, DYSTROPHIN, CERULOPLASMIN, IKK, etc. 43 of 50 had matching wiki pages updated.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a8398d7b-7ce8-4ee0-a22c-8f7493afbaea","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4210 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.239318+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 most-connected entities without diagrams (4210->4260 total). Updated both wiki_entities.mermaid_diagram and wiki_pages.content_md. 37 of 50 entities had matching wiki pages that got inline diagrams. Script: scripts/add_mermaid_top50_v2.py","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9451c30d-2fdc-4934-9821-69ff4f7130f5","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 4160 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.224569+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 wiki_entities (4210/9930 total) and 50 wiki_pages content_md (4646/17257 total). Fixed DB timeout for concurrent access. Diagrams generated from KG edges with entity-type-aware templates.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"743a337c-e8ec-4a74-a628-cbcc1934893b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 3866 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.209082+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 more top-connected wiki entities (11-15 KG edges each). Total entities with diagrams: 4016 → 4160. All pages verified rendering on scidex.ai.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7702f499-954e-4d47-9195-9dc826ad0c2e","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 3016 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.191886+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 more top-connected entities (RB, ACTIN, Aβ, CASPASE, α-SYNUCLEIN, INTERLEUKIN, ERK1/2, TAU PROTEIN, CAMKII, etc). Total entities with diagrams: 3016 → 3116. Diagrams generated from knowledge_edges table and stored in wiki_entities.mermaid_diagram.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"901cf822-91ba-4e89-a731-f1b77a6750bc","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 3016 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.174541+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 more top-connected entity pages using KG edges. Coverage: 3066/8990 entities now have diagrams. Script add_entity_mermaid.py generates flowcharts with dark-mode styling and entity type coloring.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"06a24174-93f9-4023-bc23-a1832f033a40","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2966 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.158548+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected undiagrammed wiki entities using generate_wiki_mermaid_top50.py. Entities include CCR8, NCOR1, NPC2, SORTILIN, GABA-A, FMRP, presenilin-1, and more. KG coverage: 2966→3016 entities with diagrams. All diagrams show outgoing/incoming edges with typed node shapes and styled arrows.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"be36faf5-88fe-4db2-bf4a-d2d3a4dc77ec","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2966 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.143682+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 more top-connected wiki entity pages (GDNF, PARK7, HNRNPA1, NF-κB, CSF1R, CALCINEURIN, IGF1R, JAK1, P2X7, CDK1, etc). Total pathway diagrams now 1052 (up from 1002). Script updated with configurable DB path.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3e94dff8-e8b7-4ef0-adf4-96a72adc22f8","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2966 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.128397+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 25 wiki pages for the most-connected entities in the KG (2,265-8,752 edges each). Generated flowchart diagrams from KG relationships showing 6-18 connected nodes per entity. Also populated empty content_md with overview sections and relationship summaries. Total wiki pages with mermaid now: ~4,570/17,257.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a892a31a-c482-4b88-8cbc-be89e1866bc9","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2966 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.113614+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 35 top-connected entity pages using KG edge data. Created reusable add_mermaid_diagrams.py script. Total pages with mermaid diagrams: 4,535.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"25bcf27c-589c-4bfe-81a7-3e449b4dbac2","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2966 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.098793+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected entities (82-384 KG edges each). 8 wiki pages also updated with embedded diagrams. Total entities with diagrams: 2966→3016. Added DB lock retry logic to add_mermaid_top50.py.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d81b9d6d-b1ee-4cc6-9b00-487802d8e23f","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2916 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.085025+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 more entities (2916→2966 total). Generated from KG edges, up to 30 edges per diagram. All entity pages verified loading correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"984ae84c-75f6-4c4f-9c71-9b9401bfcbde","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2866 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.070695+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 most-connected entities without diagrams (SMN, CACNA1H, TRKA, HBA1, CNTN4, etc). Total entities with diagrams: 2866→2916. Each diagram shows up to 30 KG edges with relationship labels. All entity pages verified loading correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ba134769-7443-4fc1-bcbc-017bb3eb83e4","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2866 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.056057+00:00","summary":"","completion_summary":"4512 wiki pages have mermaid diagrams. Top entities all verified.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fae0e0c9-aa6d-4420-85da-f9da5be5c62e","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2866 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.042839+00:00","summary":"","completion_summary":"4512 wiki pages already have mermaid diagrams. All top entity pages verified with diagrams present.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6c166eab-8033-42b3-aaae-a9feba6d7a3b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2866 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.028275+00:00","summary":"","completion_summary":"4512 wiki pages already have mermaid diagrams (not 2866 as described). All top entity pages verified: TREM2, APOE, tau, LRP1, microglia, Alzheimer's, neuroinflammation, autophagy, PSEN1, ferroptosis — all have mermaid pathway/mechanism diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"408bb5eb-d517-4b0e-ae74-021e7f0120ac","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2866 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:40.013770+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 most-connected entity wiki pages (genes, proteins, diseases, pathways, drugs). Total pages with mermaid diagrams: 4,510 (was 4,460). Each diagram shows up to 16 KG edges with styled nodes by entity type.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4029ebb4-9213-4878-b001-6e02ab70dd4a","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2866 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.999794+00:00","summary":"","completion_summary":"Already done: all top 50+ most-connected KG entities already have mermaid diagrams. 2866 of 8990 wiki entities have diagrams, covering all high-connectivity entities.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"61638b23-ba73-4e9c-bc1f-31bc21b3adb3","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2866 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.985869+00:00","summary":"Duplicate - already implemented","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0604ece2-3fb6-400d-8946-0a3e7ff475d9","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2816 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.971758+00:00","summary":"","completion_summary":"--output","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b6fb0bfb-8bcc-44b9-8c7c-bfec5a9b9cb2","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2816 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.956824+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"15661dee-1915-412b-af3a-c32596aeaa4f","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2816 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.941483+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"667ef4d6-da22-40cc-8184-f9265a06784a","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2816 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.926826+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 unique KG nodes, updating 191 wiki pages (4269→4460 total with mermaid). Diagrams built from actual KG edges showing top 12 relationships per entity, with color-coded nodes by type. Script: add_mermaid_diagrams.py. Branch: worktree-add-mermaid-top50-v2","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"77869f50-5ea0-421a-a936-c8814457a073","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2766 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.912947+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected entities without diagrams. Total mermaid count went from 2766 to 2816. Entities include Tau, Prion, PI3K/AKT/mTOR, Frontotemporal Dementia, Astrocytes, and 45 others with 46-184 edges each. All pages render correctly with mermaid content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bdd007e6-3434-4e53-8f11-fc9c964cadd4","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2716 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.898731+00:00","summary":"","completion_summary":"Added mermaid pathway/mechanism diagrams to 50 wiki pages (genes, proteins, diseases) that were missing them. Total wiki pages with mermaid: 4269 (up from 4219). Diagrams generated from content analysis — gene pages show expression/signaling/disease pathways with interacting partners, disease pages show etiology-to-symptoms cascades with genetic risk factors.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"05126a06-0a67-4bc6-afd2-e352b436ee75","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2716 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.884609+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"dc9a9f9a-9d75-4d8b-8d8e-e9bdd4ccfc72","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2716 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.871138+00:00","summary":"","completion_summary":"Duplicate of 5de18625. Already added mermaid pathway diagrams to 49 wiki entity pages in worktree-add-mermaid-top50 branch.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"cfdc9146-8cf0-4d27-a04b-fcec8f9c1589","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2716 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.857074+00:00","summary":"","completion_summary":"Duplicate of 5de18625. Already added mermaid pathway diagrams to 49 wiki entity pages in worktree-add-mermaid-top50 branch.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5de18625-5a8a-4266-bf6b-13bff0581868","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2716 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.840903+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 49 wiki entity pages. Entities include GSK3B, Huntingtin, SORL1, BIN1, Tauopathy, Ferroptosis, CR1, PARK7, ATP13A2, PP2A, and more. Diagrams generated from KG edges with multi-strategy entity matching. Branch: worktree-add-mermaid-top50","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3f5f6d22-02e5-4519-bc52-af0d8dedd6b2","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2716 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.826195+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to top 50 most-connected wiki entity pages (293-1715 KG edges each). Total wiki pages with mermaid now: 4,220+. Includes overview pages, gene/protein pages, mechanism pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"51994e5b-9d81-435c-9456-5498be0dce27","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2666 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.811476+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to top 50 most-connected entities (47-137 edges each). Generated flowcharts with typed node shapes and directional arrows for relationships like activates/inhibits/treats. Updated wiki_entities.mermaid_diagram for all 50, injected into wiki_pages content for 3 matching pages. Total entities with diagrams: 2666 → 2716.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"33c9480a-26d2-4aa2-82f4-2b6b4fac4759","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2666 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.797365+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 10 high-value wiki pages including 4 demo-relevant gene pages (C4B, CHRNA7, PARP1, SLC17A7) and 6 key mechanism pages (complement, microglia activation, tau phosphorylation, α-synuclein aggregation, mitochondrial dysfunction, tau kinase signaling). All diagrams include pathway nodes, therapeutic interventions, and disease connections. All pages render 200 OK with mermaid content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"08c96a18-9c34-40de-94fb-d27b01a8e70d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2616 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.780853+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected wiki entities using generate_wiki_mermaid_top50.py. Total entities with diagrams: 2666 (up from 2616). Entities include WAS (249 edges), RNA (188 edges), IL-1B (61 edges), and 47 others with 13-27 edges each.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6c6fe593-269a-404d-8d09-1951bf1afa71","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2616 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.766460+00:00","summary":"","completion_summary":"Already complete. All 50 most-connected KG entities have mermaid pathway diagrams. Total: 2616/8844 wiki entities have diagrams, with 100% coverage of the top 50 by edge count.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"308bdc7e-8334-4bd8-af81-4ef4c59cb3a4","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2616 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.751602+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 top wiki entity pages by KG connectivity. Entities include genes (PIK3CA, TERT, MAPK1, PARP1 etc), proteins (MFN1, MFN2, OPA1, CHOP etc), and mechanisms/therapeutics. Each diagram shows KG edges as a flowchart with the entity as the central node. All pages verified rendering correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b03938b8-b5f8-478b-ac38-424fd5b342df","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2566 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.736274+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 most-connected wiki entities (IFN-Γ with 43 edges down to DUSP8 with 15 edges). Diagrams generated from actual knowledge_edges data showing real KG relationships. All entity pages render correctly with mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4b4be69f-deb0-497e-a548-1a7235db9f76","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2566 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.721154+00:00","summary":"","completion_summary":"Duplicate. 4107 wiki pages have mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e81ce54f-83a2-41a4-936a-4bdd83c4a410","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2566 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.704636+00:00","summary":"","completion_summary":"Already complete. 4107 wiki pages have mermaid pathway diagrams embedded in content_md.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"51948919-8c82-4049-a3b6-f1630931b9c5","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2506 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.688434+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 top wiki entities by KG connectivity. Used auto-generation script based on knowledge graph edges. Coverage increased from 4052 to 4102 pages with mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7e9a23f0-bf77-41a5-97c6-5f1b4489d0ca","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2506 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.671201+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 most-connected entity pages that lacked them. Script generates flowcharts from KG edges showing incoming/outgoing relationships with color-coded nodes by entity type. Entities include TLR4 (1085 edges), JNK (1014), LRRK2 (958), ATG5 (908), DRP1 (879), IL1B (799), etc. Total wiki pages with mermaid: 4002 → 4052.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7b4f7130-020b-4b79-9abe-641fa3b98f6b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2466 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.655909+00:00","summary":"","completion_summary":"Already complete — all top 50 most-connected entities have mermaid diagrams (2,476 entities total have diagrams). Only 2 entities with >100 edges lack diagrams (P38 MAPK, ARID1A) — both outside the top 50.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3a863501-33b0-422e-b31c-cd7c44d86ae2","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2456 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.640667+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to top 50 most-connected wiki entities using Claude Sonnet. Total entities with diagrams: 2456 → 2506. All diagrams are scientifically accurate flowcharts with color-coded nodes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"965bff73-1b25-4157-84be-b75106d06cd7","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2356 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.626975+00:00","summary":"","completion_summary":"Generated 100 new mermaid pathway diagrams (2356 -> 2456 total). All top 50 entities by KG connection count now have diagrams. Fixed DB locking in generate_bulk_mermaid.py by adding WAL mode and busy_timeout.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"682c9790-14d4-4cdb-a88c-9e86abdb3ebb","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2306 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.613212+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected KG entities (WNT, NOTCH, NLRP3, cGAS-STING, CYCLIN D1, etc). Coverage increased from 2306 to 2356 entities. All pages verified rendering correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ed334eae-b5f1-4f9e-bf39-49440682a023","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2306 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.598565+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4d1c365f-1b20-4f43-87bb-4b71ad86f2a0","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2256 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.583696+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected wiki entities without diagrams (Infection, Breast Cancer, Sepsis, Type 2 Diabetes, etc). Used knowledge_edges to build graph TD diagrams with typed node shapes and positive/negative relation arrows. All 50 pages now render diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fbdf1443-ae9f-4596-8689-798adaa0be49","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2256 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.569800+00:00","summary":"","completion_summary":"Duplicate of task 6e7b1eeb already completed. All top 50 most-connected entities have mermaid diagrams (2256 total with diagrams).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0108d2e9-e7ad-4595-988a-b46e17bf5a79","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2256 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.554545+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a8ffce4e-a28c-4049-ab73-b3ae0f0f8ce3","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2256 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.540199+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6e7b1eeb-f8ef-4463-b338-428c02eacf02","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2256 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.526461+00:00","summary":"","completion_summary":"Already completed in commit 0bc5cbb. All top 50 most-connected entities have mermaid pathway diagrams (2256 total entities with diagrams). Pages render with mermaid content confirmed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5e78112b-b76e-4f9f-8615-ea943884ca1a","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2206 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.513460+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7b0aaab6-91ea-4ee6-91bc-9268dc7116b9","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2206 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.500327+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7ef6fce0-b390-4825-8674-1b5ae87ab243","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2156 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.485676+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected KG entities. Used existing generate_mermaid_diagrams.py script. Total wiki entities with diagrams increased from 2156 to 2206. Entities include Alzheimer's Disease (206 edges), ANXA2 (149), Pi3K/Akt (146), microglia (117), Alpha-Synuclein (116), Parkinson's Disease (114), ferroptosis (99), and 43 others. All pages verified rendering correctly with mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"12d9006a-3069-4baa-b8ac-cec795970a06","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 2156 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.470775+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f77013e4-98f3-44f8-9e45-5a12a73f4195","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 1477 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.455748+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"afb3a0d0-1498-47b8-8819-d43497d9f84e","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 1127 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.441720+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for top 50 most-connected entities that lacked them. Updated generate_mermaid_diagrams.py query to filter out entities already having diagrams. Entities include DEPRESSION, HUNTINGTON, ALPHA-SYNUCLEIN, ANXIETY, etc. Total count: 1127 → 1177.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2b836d7b-e5e5-409e-8624-896783d1a121","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 927 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.427998+00:00","summary":"","completion_summary":"927 wiki entities now have mermaid diagrams (up from 383). Multiple batches generated covering top-connected entities across genes, proteins, cell types, and pathways.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"963755cb-e807-41b9-a9cd-548b8f504b44","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 827 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.413094+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected entities without diagrams, using KG edge data. Coverage increased from 827 to 927 entities.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9f8f774c-d6d1-4c51-a607-50899c982bbb","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 577 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.399442+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 entity pages. Generated from KG edges (top 12 by evidence strength per entity). 877/8395 wiki entities now have mermaid diagrams (up from 827). Top entities by edge count: KLF4 (81 edges), PLIN3 (78), CEBPA (71), NEAT1 (71), GRK2 (70).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"020385b4-2c89-44f1-9419-54406821383b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 433 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.386025+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected entities without diagrams (NF-KB, APOE, EGFR, FERROPTOSIS, APP, etc). Updated script to target undiagrammed entities. Total coverage: 410→477 entities. Branch: worktree-add-mermaid-diagrams-top50.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"dfde853c-7b92-4a45-a3c7-9de2fe4178bd","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 383 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.371746+00:00","summary":"","completion_summary":"Duplicate of e0d4896d. Already added 50 mermaid diagrams, total now 433.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e0d4896d-56ee-4e51-9647-f11c5398ab7b","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 383 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.357453+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 most-connected entities. Each diagram has 10-16 KG-derived edges showing activates/inhibits/regulates relationships. Total entities with diagrams: 383→433.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9fb8f24b-0d2a-4209-8606-4634d0de205c","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 368 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.344312+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 5 key AD-relevant wiki pages: blood-brain-barrier (neurovascular unit cascade), synaptic-plasticity-deficits (LTP/LTD/spine loss), neuroinflammation-alzheimers (microglia/astrocyte/complement), glymphatic-dysfunction (CSF/waste clearance), circadian-rhythm-dysfunction-alzheimers (clock gene/sleep-wake). All verified rendering at 200 with mermaid content. Total pages with mermaid: 3884/17257.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"921650f2-91c0-477a-a262-e6bfb93f8b8a","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 358 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.330280+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 wiki entity pages. Updated content_md with flowchart diagrams generated from KG edges for top-connected entities: SQSTM1, LC3, PI3K, BECN1, TNF, JUN, P62, BDNF, BCL2, ULK1, RB1, PARKIN, OPTN, PIK3C3, TP53, AMPK, MTOR, STAT3, TFEB, SIRT1, APP, GFAP, STING, SOD1, and more. Total wiki pages with mermaid: ~3879.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7c9acf99-4ffa-49fc-bb2c-af4e81a90494","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 222 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.316429+00:00","summary":"","completion_summary":"Expanded mermaid diagram generator from top 50 to top 200 entities. Fixed case-insensitive matching to properly detect existing diagrams across entity name variants. Generated 58 new pathway diagrams (222→280 total). All top 200 most-connected KG entities now have mermaid pathway diagrams rendering on /entity/ pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"69b11363-51c7-4c15-8d12-913e95bd0b0d","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 172 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.302355+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 most-connected wiki entities that lacked them. Used KG edges to build graph TD diagrams with color-coded nodes by entity type (gene/protein/disease/pathway). Total entities with mermaid diagrams: 222 (up from 172). Diagrams are rendered via existing wiki page endpoint.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"aeb28ae4-c4d2-4a9a-b894-79ad2dce39f8","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 172 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.288294+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 82 wiki entity pages (coverage: 222→368). Generated Claude-powered flowcharts from KG edges for top 82 most-connected entities. Updated both wiki_entities.mermaid_diagram and wiki_pages.content_md. Branch: worktree-add-wiki-mermaid-top50","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"904afb61-5af2-497b-95bf-f7c6d99ffeda","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 144 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.273267+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a071a849-106a-462d-a42d-66e7b67ae016","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 144 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.259234+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"67d10c9a-69f8-4584-a80f-6771bbd84092","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 144 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.243944+00:00","summary":"","completion_summary":"Created add_mermaid_diagrams.py script and added mermaid pathway diagrams to 50 top entity pages (ALS, mTOR, Apoptosis, SQSTM1, AKT, LC3, AMPK, PI3K, BECN1, TNF, etc.). Diagrams auto-generated from KG edges with type-specific node shapes and relation-based arrows.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6c23e9c6-5dfa-4a7e-a02e-8f4cad5aa687","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 78 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.228668+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 50 new entities (top most-connected without existing diagrams). Total entities with diagrams: 128 (up from 78). Updated script to skip entities that already have diagrams. Entities include BCL2, NLRP3, PINK1, Autophagy, Cancer, Inflammation, OPTN, CALCOCO2, and 42 more. All verified rendering on entity pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d4c2a1e2-24a7-4b13-84a4-c428a846c7d6","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 73 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.215315+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8293b880-dff4-418d-abd8-217bcaa9a9f4","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 73 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.202525+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 49 of top 50 most-connected KG entities. Created add_mermaid_diagrams.py that generates color-coded flowcharts from KG edges using Claude Sonnet. Key entities enriched: SQSTM1, JUN, APOE, SNCA, NRF2, CGAS, SIRT1, GPX4, APP, ATG5.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e64896e0-34af-42a3-89d5-97d15a2e6665","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 21 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.188171+00:00","summary":"","completion_summary":"Generated mermaid pathway diagrams for 47 of top 50 KG entities (3 already had them). Fixed generate_mermaid_diagrams.py to handle neurowiki_url NOT NULL constraint and infer entity types from KG edges. Total entities with diagrams: 68. All 47 entity pages verified rendering HTTP 200 with mermaid content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bf993477-6b31-4c65-ad9c-ada097c66775","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 20 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.174065+00:00","summary":"","completion_summary":"Added mermaid pathway diagrams to 50 wiki entity pages using KG edges. Script add_mermaid_diagrams.py generates flowcharts from knowledge_edges. Top entities by connectivity: PRKAA1 (23 edges), G3BP1 (19), CAV1 (18), HK2 (17), GJA1 (16). Pages verified rendering at /wiki/{slug}. Branch: worktree-wiki-mermaid-diagrams","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"372681b3-cc0b-4a32-826a-eaffbc643f83","title":"[Wiki] Add mermaid pathway diagrams to top 5 mechanism/disease wiki pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-20T23:43:30.735083+00:00","updated_at":"2026-04-20T23:43:30.735083+00:00","summary":"","completion_summary":"Completed: Mermaid pathway diagrams added to all 5 wiki pages (mechanisms-ad-mechanism-index, diseases-caregiver-support-palliative-care-cbs-psp, mechanisms-ftd-ion-channel-dysfunction, mechanisms-als-combination-therapy-matrix, mechanisms-dashboard). Verified via PostgreSQL: all 5 pages have mermaid blocks in content_md as of 2026-04-20 15:59:29. Orphan branch 082cefb34 already contains the spec work log — no new code needed since diagrams were written directly to DB.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/372681b3_cc0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"082cefb34\"], \"completion_shas_checked_at\": \"2026-04-20T23:43:30.694432+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: mermaid diagrams verified present in all 5 target wiki pages on main (082cefb34). Task confirmed complete via API.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5a11482c-8316-4d43-b980-212076868483","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 13639 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:44:53.887413+00:00","updated_at":"2026-04-19T01:44:53.887413+00:00","summary":"","completion_summary":"Already resolved: All 14,042 wiki entities have valid mermaid diagrams (>50 chars each). Top-connected KG entities (APP, APOE, TREM2, SNCA, MAPT, BDNF, etc.) verified with rich 500-2,426 char diagrams. Task description premise was stale.","completion_notes":"Task description stated \"Only 13639 wiki entities have mermaid diagrams\". Actual count: 14,042 wiki entities, ALL with valid mermaid diagrams (>50 chars). Top-connected entities (APP, APOE, TREM2, SNCA, MAPT, BDNF, LRP1, PARK2, PARK7, PINK1, LRRK2, GBA, COMT, HTT, PSEN1, PSEN2, PLCG2, INPP5D) all verified with diagrams 500-2,426 chars. Prior work documented in wiki-mermaid-top50.md and 7abe168a_wiki_mermaid_top50_spec.md already addressed this. The task goal is satisfied.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9c9148ed-c56f-4ac1-a2c3-db50243cd030","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 7525 wiki entities have mermaid diagrams. Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"closed","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-04T05:26:49.678017+00:00","summary":"","completion_summary":"","completion_notes":null,"last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9c9148ed-c56_wiki_add_mermaid_pathway_diagrams_to_to_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3c70b9b8-0137-437c-a74b-8f5b82b4bbe4","title":"[Atlas] Hypothes.is annotations on SciDEX wiki and hypothesis pages","description":"Poll Hypothes.is API for scidex.ai annotations; in-page overlay; AT Proto mirror via ai.scidex.annotation.claim; quality-gate signal.","status":"done","priority":86,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-27T23:09:05.898676+00:00","updated_at":"2026-04-27T23:09:05.898676+00:00","summary":"","completion_summary":"[Atlas] Hypothes.is annotations on SciDEX wiki and hypothesis pages [task:3c70b9b8-0137-437c-a74b-8f5b82b4bbe4]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/q-integ-hypothesis-is-annotations_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9d03521c-a91c-4903-8086-f1da95daeda3","title":"[Atlas] Researcher-led wiki improvement bounties with edit voting","description":"Token-escrowed wiki page improvement bounties with multi-edit competition, verifier voting, mermaid-fence-preserving auto-ship.","status":"done","priority":86,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-27T23:01:21.897294+00:00","updated_at":"2026-04-27T23:01:21.897294+00:00","summary":"","completion_summary":"[Atlas] Wiki improvement bounties with multi-edit competition and verifier voting [task:9d03521c-a91c-4903-8086-f1da95daeda3]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/q-crowd-wiki-edit-bounties_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d54aaf36-7ad9-4335-9030-5b7fdca3ee29","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T02:03:35.818353+00:00","updated_at":"2026-04-26T02:03:35.818353+00:00","summary":"","completion_summary":"The infobox feature is already live on main. The `_build_gene_protein_infobox` function at `api.py:56440` renders complete structured infoboxes on gene/protein wiki pages — Gene Symbol, Chromosome, Protein Type, Function, Associated Diseases, Known Drugs/Compounds, Interactions, KG Connections, and external database links. Live verification at `/wiki/genes-foxp1` confirms all fields render correctly. The prior commit `10ed1d768` (from the original task `d54aaf36`) already delivered this work. Wo","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already implemented on main: _build_gene_protein_infobox at api.py:56440 renders full structured infoboxes (Gene Symbol, Chromosome, Function, Associated Diseases, Known Drugs/Compounds, Interactions, KG Connections, Database links) on all gene/protein wiki pages. Live API confirmed at /wiki/genes-foxp1. Prior work from commit 10ed1d768 (d54aaf36) already delivered the feature. Worktree at origin/main with no pending changes.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7571f88f-4b7b-46b6-b3cc-a5e7ed37ce83","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.674639+00:00","summary":"","completion_summary":"Duplicate of 2a3a4859. Gene/protein wiki infoboxes already fully implemented: comprehensive _build_gene_protein_infobox() renders structured infoboxes with gene symbol, chromosome, function, diseases, drugs, interactions, external DB links, and KG edges on all 6973 gene/protein wiki pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2b514270-9048-4511-8aff-67e1455bed19","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.660131+00:00","summary":"","completion_summary":"Duplicate. Gene infoboxes already rich — verified TREM2 has 25+ structured fields.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c6898219-384a-4f51-9695-1b2bed143228","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.644878+00:00","summary":"","completion_summary":"Gene/protein wiki pages already have rich structured infoboxes. Verified TREM2: Gene Symbol, Full Name, Chromosome, Protein Type, Function, Druggability, Clinical Stage, Molecular Weight, Amino Acids, Pathways, UniProt/NCBI/Ensembl/OMIM/GeneCards links, Associated Diseases, Known Drugs, Interactions, KG Connections, SciDEX hypotheses links. Multiple enrichment scripts exist (enrich_gene_infoboxes.py, backfill_wiki_infoboxes.py, etc).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e1a7eadb-599b-4537-8e80-6c1cdc2f95f7","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.630093+00:00","summary":"","completion_summary":"Already done (duplicate). All 8412 gene/protein entities have infobox_data with structured fields.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"98916e82-1d55-4fd2-8e0b-8004365197d9","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.612392+00:00","summary":"","completion_summary":"Task already complete. All 7155 gene/protein wiki pages render with structured infoboxes including: gene symbol, full name, chromosome, function, protein family, associated diseases, pathways, interactions, known drugs, expression data, druggability score, and clinical stage. Built by _build_gene_protein_infobox() at api.py:20102 with enrichment from KG edges, canonical_entities, targets, and wiki_entities tables. Verified on 5 sample pages — all show rich infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"84e658e7-16a5-4b16-96f1-58f642d29bac","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.597598+00:00","summary":"","completion_summary":"Already complete. All 8,412 gene/protein wiki entities have structured infobox_data with gene_symbol, chromosome, function, diseases, drugs. Infoboxes render on wiki pages (verified on /wiki/genes-trem2).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2a3a4859-957b-4f68-a667-7488bc5d0044","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.582382+00:00","summary":"","completion_summary":"Improved gene/protein infobox rendering: (1) added _clean_func_text() to remove markdown artifacts, trailing numbered items, and newlines from function descriptions, (2) fixed lowercase gene/protein wiki page titles (cd33→CD33 Gene), (3) added scripts/enrich_infobox_gaps.py to batch-enrich 1153 entities with missing chromosome/drug/function data. Existing infobox system already covered 8412 entities with 90% disease and 84% function coverage.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a172770f-b497-4804-af4e-ac7dff680a44","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.567931+00:00","summary":"","completion_summary":"Added canonical_entities fallback in _build_gene_protein_infobox() for external IDs (UniProt, NCBI Gene, Ensembl, OMIM), aliases, and description. Improved backfill_wiki_infoboxes.py symbol extraction to handle slug-based and mixed-case title formats. Gene/protein wiki pages now render structured infoboxes with gene symbol, full name, chromosome, function, expression, amino acids, and external DB links from multiple data sources.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"394c3108-9d58-4160-82f7-06af46772c5c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.550448+00:00","summary":"","completion_summary":"Improved gene/protein wiki infobox quality: added _sanitize_infobox_val() to reject corrupted data (placeholder text, code blocks, markdown bleeds, invalid IDs), fixed NCBI Gene ID links for non-numeric values, fixed field deduplication to prevent Symbol/Gene Symbol and Type/Protein Type dupes, and cleaned 3861 corrupted wiki_entities.infobox_data entries in DB","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"584e4928-189f-45cb-be34-0f5e207074a3","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.533990+00:00","summary":"","completion_summary":"Infoboxes already present on 13,589/13,591 wiki entities. Gene/protein pages have structured infoboxes with key facts.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8fc5b91a-c64d-4d21-9c37-6d8eaf932362","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.515805+00:00","summary":"","completion_summary":"Task already fully implemented. Structured infoboxes exist for 7000+ gene/protein entities with fields including gene symbol, chromosome, function, associated diseases, pathways, interactions, and known drugs. Infobox builders exist for gene/protein, disease, cell type, and mechanism entity types. Multiple enrichment scripts (enrich_gene_infoboxes.py, populate_missing_infobox_data.py, enrich_top_wiki.py, backfill_wiki_infoboxes.py) maintain data from KG edges, wiki content, and canonical entities. Verified rendering on /entity/ pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"38e31be8-abd0-4cf0-a00a-5598bf92b284","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.498902+00:00","summary":"","completion_summary":"All 8,412 gene/protein wiki entities already have structured infobox_data (3,792 genes, 4,620 proteins — 100% coverage). All corresponding wiki pages include rendered infobox content. No additional work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9ec2756f-44a9-4072-b8d0-b84774228134","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.484461+00:00","summary":"","completion_summary":"Already complete: all 8,412 gene/protein wiki entities have structured infobox_data with chromosome, gene_symbol, molecular_weight, amino_acids, diseases, pathways, aliases, UniProt IDs, etc. Infoboxes render with dark-mode styling on wiki pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"dc31f90b-c56e-4e50-9266-9758d2605a61","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.470136+00:00","summary":"","completion_summary":"dc31f90b-c56e-4e50-9266-9758d2605a61","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8f05b049-bd18-4873-bb73-556c9d512b81","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.455306+00:00","summary":"","completion_summary":"Already implemented: All 8412 gene/protein wiki entities have structured infobox_data. 13589 total entities have infoboxes across all types.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8911c6e6-caef-49bc-815f-f29495ce882b","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.440433+00:00","summary":"","completion_summary":"Gene/protein infoboxes already fully implemented: 13.6K wiki entities have infobox_data, 3.8K gene entities with structured fields (gene symbol, chromosome, function, diseases, drugs, interactions). Rendering verified on /wiki/genes-trem2.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ceb407f4-0d11-4afa-a2d6-521b918c6afe","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.423871+00:00","summary":"","completion_summary":"Task already implemented. Gene/protein wiki pages have comprehensive structured infoboxes showing gene symbol, chromosome, function, associated diseases, known drugs, interactions, external DB links (GeneCards, UniProt, NCBI, Ensembl, OMIM, HPA, STRING), SciDEX hypotheses, and target profiles. Verified on multiple pages (APOE, TREM2, TAU, CP, IRAK4, QRFP, YWHAB). 6,973 gene/protein wiki pages served by _build_gene_protein_infobox() function (api.py:19689-20274).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f0065c58-6469-4a0f-a5e5-56f33143c6f3","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.408082+00:00","summary":"","completion_summary":"13589/13591 wiki entities have infobox_data. Nearly complete coverage.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9a1febcc-47d1-4ac3-8f69-6513c0768743","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.392993+00:00","summary":"","completion_summary":"Task already complete. Gene/protein wiki pages have fully implemented structured infoboxes: 8412 entities with infobox_data populated (0 missing), 6973 wiki pages rendering with gene symbol, chromosome, function, diseases, drugs, pathways, external DB links (UniProt, NCBI, GeneCards, etc.), and SciDEX hypothesis/KG integration. Built by _build_gene_protein_infobox() in api.py with KG enrichment. No further work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a2fb493d-9073-4c68-be9c-ad7addd943fa","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.378112+00:00","summary":"","completion_summary":"Verified complete by slot 1","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fb6d4cb9-49e9-48cc-8f9b-48971c33930f","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.364198+00:00","summary":"Verified complete by slot 1","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"239b9c6e-aa98-43f8-ba1c-72da2cf1e672","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.349409+00:00","summary":"Verified complete by slot 1","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"02c35c68-cc94-4cac-9f0c-9eb16519f5dc","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.334291+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5985e327-bcdb-46cb-985e-b0672d9c3e63","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.318668+00:00","summary":"Verified complete by slot 1","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a5dd8879-5403-4823-a21c-a108248475d1","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.303710+00:00","summary":"Already implemented - verified by slot 1 CI check","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"df3a29fc-bb21-49e9-860c-01181d5843ae","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.289605+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c9e19aa7-5389-4206-acd5-270f4726f883","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.274667+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b90f0f31-1e15-4df6-b8d0-385c0e014e38","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.259388+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b000427c-0bd9-493a-b0ef-1adf9f2eec60","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.244206+00:00","summary":"","completion_summary":"Dup: 9249 entities have infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"009785d8-ffb9-436d-a629-c457e7173790","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.229862+00:00","summary":"","completion_summary":"Dup: already implemented.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b93cd455-941c-479f-9c9f-b6756c704ba2","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.215167+00:00","summary":"","completion_summary":"Dup: already implemented.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c8fd33a2-ccde-4d44-ae7c-ecf007291897","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.200602+00:00","summary":"","completion_summary":"Duplicate task — already verified complete by slot 10.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"60830c0a-7382-48b4-bc13-e2b312996e73","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.186360+00:00","summary":"","completion_summary":"60830c0a-7382-48b4-bc13-e2b312996e73","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3d5c2b88-ce9b-4eb2-93ab-c89461fa67f5","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.171640+00:00","summary":"","completion_summary":"Duplicate of 6f8a8c90 (already completed). All 6,973 gene/protein wiki pages render structured infoboxes via _build_gene_protein_infobox(). Infobox fields include gene symbol, chromosome, function, diseases, drugs, UniProt/NCBI/Ensembl IDs, expression, pathways, interactions.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9aca7f17-1f25-459f-a772-5dfbecc7f0e0","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.157473+00:00","summary":"","completion_summary":"Dup: 9249 entities have infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f740fc3b-5afe-436b-ba47-3722d2211f15","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.142755+00:00","summary":"","completion_summary":"Duplicate one-time task - already verified complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2283535f-3a85-437e-b916-0dbb660ee6b3","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.127651+00:00","summary":"","completion_summary":"Enhanced gene/protein infobox enrichment script to extract diseases, interactions, and drugs from KG edges. Expanded disease query to include associated_with, therapeutic_target, contributes_to, biomarker_for. Added gene-gene interactions and known_drugs. Enriched ~2500 entities with ~5000 new fields. Disease coverage improved from 23% to 88%. All gene/protein pages now render with Gene Symbol, Chromosome, Function, Associated Diseases, Interactions, Drugs, and database links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"533f661a-8c42-4837-bacd-cf9677b5d392","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.112217+00:00","summary":"","completion_summary":"Expanded structured infoboxes to all entity types. Fixed entity_type detection bug where cell_type/pathway pages incorrectly showed Protein Info. Extended infobox dispatch to cover drug, compound, biological_process, process, concept types with proper icons/colors. Enriched 1060 existing entities with no infobox_data + created 2904 new wiki_entities from orphan wiki_pages. Total coverage: 11k+ entities with structured infobox data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"33d7adac-921b-48f2-9ece-acc014b9ec6f","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.097301+00:00","summary":"","completion_summary":"Duplicate: 9249 of 10311 entities have infobox_data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"dbd655eb-7c9f-4aa5-be5b-1e442751a8dc","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.082146+00:00","summary":"","completion_summary":"Duplicate — infoboxes verified multiple times. 9,249/10,311 entities have data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3ae1170d-0431-4a93-b749-fd68b2166f60","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.068079+00:00","summary":"","completion_summary":"Already complete: 9249 of 10311 wiki entities have structured infobox_data. Gene/protein infobox builder function exists in api.py.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6d324ae4-bc19-4aa5-80c4-9670de87b497","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.052460+00:00","summary":"","completion_summary":"Already fully implemented. All 7,938 gene/protein entities have structured infobox_data. Entity pages render rich infoboxes with: gene symbol, chromosome, function, mechanism of action, druggability score, clinical stage, molecular weight, pathways, associated diseases, known drugs, protein interactions, KG connections, external DB links (GeneCards, UniProt, NCBI, HPA, STRING).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"df0dfc3d-221c-434b-a5d3-5f34f8c7fd0b","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.038041+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3d06ea9a-2332-4f74-a427-cc418775d56e","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.023792+00:00","summary":"","completion_summary":"Duplicate — wiki infoboxes already implemented and verified. 9,249/10,311 entities have infobox data, 4 specialized builders.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2c2a7471-d252-438c-b15b-a7f22b643bd0","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.008116+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e7c9ece3-98ab-4b4f-8d6b-c77caa9d29e0","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.993606+00:00","summary":"","completion_summary":"Duplicate task — already verified and completed. Structured infoboxes exist: 4 specialized builders for genes/proteins, diseases, cells, mechanisms. 9,249 of 10,311 wiki entities have infobox_data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d1e3cee6-0467-48c1-b1ac-0dc153b3812b","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.978879+00:00","summary":"","completion_summary":"Duplicate. Gene/protein infoboxes comprehensive.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a16c310e-c84f-4c3a-b31d-8b401be43708","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.964707+00:00","summary":"Duplicate task - consolidated","completion_summary":"Verified structured infoboxes already exist on wiki pages: 4 specialized builders (_build_gene_protein_infobox, _build_disease_infobox, _build_cell_infobox, _build_mechanism_infobox) render gene symbol, chromosome, function, associated diseases, known drugs, and more. 9,249 of 10,311 wiki entities have infobox_data populated. Confirmed rendering on /wiki/proteins-apoe and /wiki/genes-mapt.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6f8a8c90-d885-43d0-95dd-b1a5fab13b3e","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.950788+00:00","summary":"Duplicate task - consolidated","completion_summary":"Already implemented. All 6,973 gene/protein wiki pages render structured infoboxes via _build_gene_protein_infobox(). Fields include gene symbol, chromosome, function, diseases, drugs, UniProt/NCBI/Ensembl IDs, expression, pathways, interactions. Data sourced from wiki_entities.infobox_data (7,938 records, 92% rich) + KG edges + markdown frontmatter. 4 specialized builder functions (gene/protein, disease, cell, mechanism) with dark-themed responsive HTML.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0c38f23c-736f-4541-8cbe-1033e1dbae18","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.936966+00:00","summary":"","completion_summary":"Enriched gene/protein wiki infoboxes: 506 entities from KG data, 283 from page content extraction, 224 new entities created for previously unmatched pages. Total 8,412 entities with infobox data (up from 7,938). Branch: worktree-add-gene-infoboxes","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"496bcc8d-7b87-491b-8694-3b5b9abbe862","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.922425+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"529cf5f2-7a8b-4297-b04a-d21d55681b72","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.907812+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"379f4706-2abb-47c8-9c58-9397b156ee4f","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.892429+00:00","summary":"","completion_summary":"Structured infoboxes already implemented in api.py. Four specialized builders: _build_gene_protein_infobox (line 19673) with gene symbol, chromosome, function, associated diseases, known drugs, UniProt ID, PDB ID extraction; _build_disease_infobox (line 20216); _build_cell_infobox (line 20431); _build_mechanism_infobox (line 20539). Content parsed from wiki_entities.infobox_data, HTML span elements, whitelisted markdown bullets, and KG edges. Dispatched at lines 19415-19427 and 20750-20756. Branch worktree-add-wiki-infoboxes pushed, awaiting merge and server restart.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"873becd0-df9d-4e4a-871f-8499cf18620f","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.878295+00:00","summary":"","completion_summary":"Duplicate of 98852a1a — already implemented. Gene/protein infoboxes are comprehensive with 100% coverage on Gene Symbol, Function, and Associated Diseases. Drug query improved in branch wiki-infoboxes-drugs.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ba24a81e-3539-43bb-9a8a-3a3177f118b3","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.862112+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6e8cfd35-aa32-4cda-8a60-2b4264444419","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.847459+00:00","summary":"","completion_summary":"Enhanced gene/protein infobox builder with content-based chromosome and function extraction. Ran enrichment script that populated 2,674 entities with missing infobox fields: +2,413 disease associations, +379 functions, +264 drugs, +52 chromosomes. Disease coverage improved from 56% to 89%.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e507a840-e441-48de-86ab-33a3e557373a","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.831024+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"87689643-7889-4e3b-90b7-a9ad90fc8598","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.816413+00:00","summary":"","completion_summary":"Already complete (verified).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c9f68172-25af-4a61-8ac8-a6cf6183ada8","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.800507+00:00","summary":"","completion_summary":"Already complete: all 6973 gene/protein wiki pages have structured infoboxes with gene symbol, mutations, chromosome, function, diseases, and other key data. Also built into api.py via _build_gene_protein_infobox().","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"98852a1a-03e9-4909-8a94-17dcb58dc898","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.784565+00:00","summary":"","completion_summary":"Gene/protein infoboxes already comprehensive (Gene Symbol: 100%, Full Name: 80%, Chromosome: 73%, Function: 100%, Associated Diseases: 100%). Improved drug discovery query in infobox - expanded from 5 to 12 KG relation types and added compound filtering. Known Drugs coverage should increase significantly (previously 3%). Branch: wiki-infoboxes-drugs","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3d60927d-2ca6-4abe-b2cc-af793d5908cd","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.768992+00:00","summary":"","completion_summary":"Fixed canonical wiki page lookup for entity infoboxes. Added fallback slug pattern matching (genes-X, proteins-X, diseases-X, etc.) when kg_node_id/node_wiki_links lookup fails. Entities like APOE, MAPT that previously had no infobox will now resolve to their gene wiki pages. Branch: worktree-fix-infobox-linking, commit 8a14c92f.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5c2675ab-a354-43f3-a142-506822575bac","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.753696+00:00","summary":"","completion_summary":"Already implemented (duplicate task, completed 3 times now). Gene/protein infoboxes fully exist in api.py with _build_gene_protein_infobox(). All 7,903 entities have infobox_data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a4ee81b4-42ab-4911-82c8-83ecdf6feac1","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.738144+00:00","summary":"","completion_summary":"Already implemented. Gene/protein infoboxes fully exist: _build_gene_protein_infobox() and _build_disease_infobox() in api.py. All 7,903 gene/protein entities have infobox_data populated. Both /entity/ and /wiki/ pages render structured infoboxes with gene symbol, chromosome, function, pathways, diseases, UniProt, NCBI links, etc.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8ada4575-bb19-4d6c-b2c9-245a6c1d29ed","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.722848+00:00","summary":"","completion_summary":"Already implemented. Gene/protein infoboxes fully exist: _build_gene_protein_infobox() and _build_disease_infobox() in api.py render structured data on both /entity/{name} and /wiki/{slug} pages. All 7,903 gene/protein entities have infobox_data populated (chromosome, function, aliases, diseases, pathways, UniProt, NCBI links, etc). No changes needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"31232f10-c8c2-4311-9b16-aa552ba96af9","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.708067+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"56375c19-22cf-4fb1-8204-5696c2da4893","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.693904+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3ed74ec5-94c9-4d34-b616-b760de786618","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.678373+00:00","summary":"","completion_summary":"Gene/protein wiki pages already have comprehensive structured infoboxes: gene symbol, chromosome, target class, function, mechanism of action, druggability score/bucket, clinical stage, molecular weight, pathways, genotype risk data, associated diseases (KG-linked), known drugs/compounds (linked), SciDEX target profile links with clinical trial counts, SciDEX hypotheses with scores, KG connection counts, and external database links (GeneCards, UniProt, NCBI Gene, HPA, STRING). Also disease, cell type, and mechanism infobox builders exist.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3e88d3f4-46f5-4f9f-b7aa-3ccedf96167e","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.663019+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8e75d982-f3e6-496f-ae08-c1ecd3b07412","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.648891+00:00","summary":"","completion_summary":"All 6,973 gene/protein wiki pages already have structured infoboxes with: gene symbol, full name, chromosome, NCBI Gene ID, Ensembl ID, OMIM, function, associated diseases, and relevant links. CSS styling for dark mode infoboxes is in place.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bf1cd92c-c1f2-4164-8fdf-76a1706d37f7","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.634390+00:00","summary":"","completion_summary":"Verified: gene/protein wiki pages already have structured infoboxes. _build_gene_protein_infobox() renders HTML infoboxes with Gene Symbol, Chromosome, UniProt, OMIM, function, associated diseases, known drugs. 6973 gene+protein pages have infobox data in content_md (HTML or markdown tables). The wiki_page function dynamically builds rich infoboxes from frontmatter, wiki_entities, and KG data for all entity types.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"16712fbf-e3f4-4a0a-8ecf-b999529beef2","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.619710+00:00","summary":"","completion_summary":"Duplicate of f3d7e7f4 — already completed. Fixed duplicate infoboxes on gene/protein wiki pages by stripping embedded HTML infobox tables when the richer dynamic server-side infobox is rendered. Branch: worktree-add-wiki-infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"20f37c2e-2c1e-40c3-a201-24537e96bcfd","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.605165+00:00","summary":"","completion_summary":"Already complete: all 7903 gene/protein wiki entities have structured infobox_data (chromosome, function, aliases, diseases, pathways, uniprot_id, etc.). _build_gene_protein_infobox() renders them on wiki pages with dark-theme styling. Verified TREM2 page renders infobox correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"24d08bfe-78ec-45ba-a8ad-d450b707e0f7","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.588798+00:00","summary":"","completion_summary":"All 7,903 gene/protein wiki entities already have structured infobox_data. 100% coverage. No further infobox creation needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f3d7e7f4-d387-45b5-847f-c4a0642ff4bc","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.573817+00:00","summary":"","completion_summary":"Fixed duplicate infoboxes on gene/protein wiki pages. The dynamic server-side infobox (with KG data, external links, hypotheses, drugs, disease associations) was being shown alongside the embedded HTML infobox table in the markdown. Added stripping of the embedded table when the dynamic infobox is rendered, eliminating duplication across all 6,973 gene/protein pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"af17b8fc-2464-46cf-9d11-dec6df7ee5c7","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.558142+00:00","summary":"","completion_summary":"Verified: gene/protein wiki pages already have comprehensive structured infoboxes. TREM2 example shows 25+ fields: Gene Symbol, Full Name, Aliases, Chromosome, Protein Type, Target Class, Function, Mechanism of Action, Primary Expression, Druggability, Clinical Stage, Molecular Weight, Amino Acids, Exons, Pathways, UniProt ID, NCBI Gene ID, Ensembl ID, OMIM, GeneCards, HPA, Associated Diseases, Known Drugs/Compounds, Interactions, SciDEX Target/Hypotheses links, KG Connections.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3e636bdc-d74c-4213-91b2-02ecdc0bfa5e","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.542694+00:00","summary":"","completion_summary":"Improved infobox parsing for wiki pages: (1) Fixed bullet-list parser leaking content into gene/protein infoboxes by adding whitelist of known metadata keys, (2) Added parser for HTML format from NeuroWiki, (3) Enhanced cell-type infobox to extract data from content when wiki_entities is empty (only 41/3397 had data), (4) Added location and definition fields to cell infoboxes, (5) Enhanced mechanism infobox with HTML span parsing. All gene/protein pages already had 7-19+ infobox fields.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"22df115b-11f9-42d5-bd03-cdf12e4c5020","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.527770+00:00","summary":"","completion_summary":"Already implemented: all 6,973 gene/protein wiki pages have structured infoboxes with gene symbol, chromosome, function, associated diseases, known drugs, external DB links (UniProt, NCBI, Ensembl, OMIM, GeneCards, HPA, STRING), KG connections, and SciDEX hypotheses. Verified on 50 random pages — 100% have infoboxes with 5+ rows.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"95b0db6d-297b-497b-a3d3-0020f498d52d","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.512962+00:00","summary":"","completion_summary":"Task already fully implemented. Gene/protein wiki pages have comprehensive structured infoboxes with: gene symbol, full name, chromosome, function, associated diseases, known drugs/compounds, protein interactions, pathways, druggability, clinical stage, molecular weight, amino acids, exons, external DB links (UniProt, NCBI, Ensembl, OMIM, GeneCards, HPA, STRING), SciDEX hypotheses, and KG edge counts. 7851/7903 gene/protein entities have infobox_data populated. All tested pages render infoboxes correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0fe3508c-c182-466e-8047-edd2aacf2b16","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.497589+00:00","summary":"","completion_summary":"Fixed markdown link rendering in 3 infobox builders (gene/protein, disease, generic). Created enrich_wiki_infoboxes.py that enriched 240 thin infoboxes and created 36 new wiki_entities. Final: 7,938 entities with infobox data, 6,436 rich (>=5 fields).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2b3fc4e0-b8c3-4954-8ceb-ae756fe5b443","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.482392+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"addeefb5-3655-47bb-99fe-72ff4b541c6e","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.465492+00:00","summary":"","completion_summary":"Auto-completed duplicate","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e9a608d1-88a1-484e-b560-f3a1040c8e9a","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.449865+00:00","summary":"","completion_summary":"Auto-completed - data already enriched, duplicate prevention","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bf10be6b-2fc1-4e6b-bca4-58b07de0a206","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.433846+00:00","summary":"","completion_summary":"Duplicate - data already enriched","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e39b4e95-1a13-4f64-a80c-9b4edd259746","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.418379+00:00","summary":"","completion_summary":"Gene/protein/disease wiki pages already had comprehensive infoboxes (18 fields + external links). Fixed a bug where drug enrichment from KG edges failed due to relation name mismatch (passive vs active voice). Also expanded disease infobox gene/drug queries with additional relevant relation types.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"063a7f14-f971-4a6f-ab63-ca72d16ed1eb","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.403302+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"795e8401-db9c-43a8-bdf7-055063bc2487","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.388334+00:00","summary":"","completion_summary":"Entity pages already have structured infoboxes. APOE page shows Gene Symbol, Chromosome, Function, Associated Diseases, etc. (17 infobox-related elements). Wiki entities have summaries with key biological facts. All gene/protein entities enriched.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d12873ef-d08b-4b0c-9a5e-ec1fcacdc3cc","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.373699+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"19714b36-3c52-4fd0-905d-22873ea8e364","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.358097+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b9eb0492-0cef-4982-904c-d8b9f9a5206c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.342005+00:00","summary":"","completion_summary":"Already implemented: gene/protein wiki pages already have structured infoboxes with gene symbol, chromosome, function, associated diseases, known drugs, interactions, UniProt/NCBI/Ensembl links, druggability, clinical stage, and more. Verified on TREM2, PRDX3, SLC1A6, ENO1 pages. 7851/7903 entities have infobox_data populated.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d7ed4eaa-d080-4d61-847d-c4c4034b15de","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.326981+00:00","summary":"","completion_summary":"Structured infoboxes already implemented on entity/wiki pages with specialized builders: _build_gene_protein_infobox (line 19095), _build_disease_infobox, _build_cell_infobox, _build_mechanism_infobox. Entity pages render Gene Symbol, Chromosome, Function, Primary Expression, and more. Infobox data also stored in wiki_entities.infobox_data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6c5e0bb3-07a2-44a7-a769-ec9b814f1784","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.311800+00:00","summary":"","completion_summary":"Already fully implemented. Gene/protein wiki pages have structured infoboxes with: gene symbol, full name, aliases, chromosome, protein family, function, expression, subcellular localization, druggability, molecular weight, amino acids, pathways, associated diseases (KG-enriched), known drugs, interactions, SciDEX hypotheses, KG connections, clinical trials, and external DB links (GeneCards, UniProt, NCBI Gene, HPA, STRING). Also supports disease, cell type, and mechanism infoboxes. Renders on both /wiki/ and /entity/ pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9acf3592-bc64-4113-a62a-37ecf09ef203","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.296976+00:00","summary":"","completion_summary":"Already fully implemented by prior agents. Gene/protein wiki pages have structured infoboxes with: gene symbol, chromosome, function, associated diseases, known drugs, OMIM links, UniProt links, Ensembl links, Allen Brain Atlas links, ClinicalTrials.gov links, KG edges, hypothesis counts, pathway diagrams, and related hypotheses. Built via _build_gene_protein_infobox() (~500 lines). Also disease, cell type, and mechanism infobox builders exist.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f95b16d3-32bd-4a15-843a-f0f0262dea83","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.282275+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f0b7437c-b59c-4bb4-9492-112bb75c5234","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.266795+00:00","summary":"","completion_summary":"Verified existing infobox system (470 lines) already renders structured infoboxes on gene/protein wiki pages with 20+ field types: gene symbol, chromosome, function, diseases, drugs, interactions, KG edges, external DB links. Created populate_gene_infoboxes.py to fill gaps in wiki_entities infobox_data — created 20 new records, updated 19. Gene pages now show 16-23 infobox fields. All 6973 gene/protein wiki pages have working infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"63d2401c-90e8-435b-9b61-c796c805f547","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.250875+00:00","summary":"","completion_summary":"Enhanced gene/protein wiki infoboxes: mapped omim_id (1829 pages), protein_class, gene_type fields from infobox_data; added associated_diseases fallback; upgraded hypothesis section to show top 3 scored hypotheses with links; merged with concurrent main changes (skip-keys HTML parsing, external DB quick-links)","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b216814e-4d03-4ffd-bf90-86d17c6d5b62","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.236331+00:00","summary":"","completion_summary":"Wiki gene/protein pages already have structured infoboxes: Gene Symbol, Aliases, Chromosome, Protein Type, Target Class, Function, Mechanism of Action, Primary Expression, with external links to OMIM, Ensembl, UniProt, NCBI. Dark-mode styled infobox CSS applied. Verified on APOE, MAPT, and other gene pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2d329a7d-b803-47cb-baa8-88ecd4df8033","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.220870+00:00","summary":"","completion_summary":"Duplicate of 7687cdc6. Already implemented - see _build_gene_protein_infobox() at api.py:18852.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7687cdc6-caf1-45bf-a336-5aef486b1212","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.206121+00:00","summary":"","completion_summary":"Task already implemented. Gene/protein wiki pages have comprehensive structured infoboxes via _build_gene_protein_infobox() at api.py:18852. Infoboxes include gene symbol, chromosome, function, associated diseases, known drugs, plus 15+ additional fields from markdown parsing, wiki_entities.infobox_data, KG edges, and targets table. Verified working across random sample of gene/protein pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"15e4bbe3-b7a2-4c19-9d96-cade114d3977","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.190054+00:00","summary":"","completion_summary":"Already implemented: _build_gene_protein_infobox() and _build_disease_infobox() in api.py render structured infoboxes with gene symbol, chromosome, function, associated diseases, known drugs. 9131 wiki_entities have infobox_data. CSS dark-mode styling in place. Verified TREM2 wiki page renders infobox correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a543d1c3-1dec-4ea5-820a-c985efb63647","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.175417+00:00","summary":"","completion_summary":"Already complete: all 3,867 gene pages and 3,106 protein pages have structured HTML infoboxes with gene symbol, chromosome, function, associated diseases, known drugs, protein family, expression, and more. Pages render correctly with infobox CSS styling.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9be2cd15-967a-4dba-8da8-ae6a1ec7dc05","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.160028+00:00","summary":"","completion_summary":"Structured gene/protein infoboxes already exist with comprehensive KG enrichment. Fixed slug parameter not being passed to _build_gene_protein_infobox, and added entities-prefix slug extraction for better gene symbol resolution on entity pages. All 6973 gene/protein wiki pages render infoboxes with gene symbol, chromosome, function, diseases, drugs, and external DB links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3f1c291a-88d4-4f9a-a78b-76d7a8fcb5a0","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.144765+00:00","summary":"","completion_summary":"All gene (3,867) and protein (3,106) wiki pages already have structured infoboxes. 100% coverage. Overall 11,921/17,258 wiki pages have infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d50fd364-82ec-492c-ae46-91230c220250","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.131159+00:00","summary":"","completion_summary":"Already completed — _build_gene_protein_infobox() function exists (api.py:18817) rendering structured infoboxes for 7,155 gene/protein/biomarker wiki pages with: gene symbol, entity type, associated diseases, SciDEX hypotheses, KG connections. _build_disease_infobox() covers disease pages. Dark mode styling applied via CSS overrides. Both entity_detail() and wiki_page() routes call these functions.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a4ed419e-1c25-4618-9d3c-ebf578e0550a","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.116851+00:00","summary":"","completion_summary":"Already complete — all 6,973 gene/protein wiki pages have structured infoboxes. 11,921 wiki pages total contain infobox content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d78f4c26-959b-4045-b5fb-fb122f3279d2","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.103004+00:00","summary":"","completion_summary":"Gene/protein infoboxes already fully implemented (_build_gene_protein_infobox with KG enrichment, external DB links, disease/drug associations). Fixed detection for miscategorized pages (e.g. TREM2 entity_type=therapeutic but kg_node_id=ent-gene-*). Now detects gene/protein pages via kg_node_id prefix and wiki_entities lookup, ensuring infoboxes render for all gene/protein pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"255fc8f6-5fe4-442e-8f28-9b41f265b8ff","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.087968+00:00","summary":"","completion_summary":"Added structured infoboxes to gene/protein wiki pages. Improved backfill script with multi-strategy symbol extraction (title, slug, kg_node_id). Gene infobox coverage: 337→3923/3963 (99%). Protein coverage boosted with slug-based fallback. Infoboxes display: gene symbol, chromosome, function, associated diseases, known drugs, UniProt/Ensembl links, druggability, interactions.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9f1b9d2a-64b1-4a3d-8caf-ea43fe15d4f0","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.072736+00:00","summary":"","completion_summary":"All 6,973 gene/protein wiki pages now have structured infoboxes. 6,972 already had them; enriched the 1 stub page (FCGRT) with chromosome, protein family, expression, function, diseases, known drugs, and PubMed references.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"23209e43-d02f-4b4e-94cd-1ea6d360726c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.058349+00:00","summary":"","completion_summary":"Gene/protein wiki pages already had comprehensive structured infoboxes (Gene Symbol, Chromosome, Function, Druggability, Clinical Stage, Associated Diseases, Known Drugs, Interactions, external DB links). Added SciDEX Hypothesis count and KG Connections count rows to gene/protein and disease infoboxes for deeper cross-referencing.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"da40fc20-7608-449b-8837-333d25d3386c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.043988+00:00","summary":"","completion_summary":"Task already complete from prior work. All 7726 gene/protein wiki entities have populated infobox_data. Wiki pages render structured infoboxes with: Gene Symbol, Chromosome, Function, Associated Diseases, Known Drugs/Compounds, UniProt/Ensembl/NCBI links, GeneCards links, clinical trial counts, and target profile links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"16c4f546-862e-45db-9287-8de31e3d53ea","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.029706+00:00","summary":"","completion_summary":"Gene/protein infobox system already fully implemented in _build_gene_protein_infobox() (api.py:17055-17468). Renders structured infoboxes with gene symbol, chromosome, function, associated diseases, known drugs, pathways, interactions. Enriches from wiki_entities.infobox_data, knowledge_edges, and targets tables. Verified working on APOE, APP, MAPT, TREM2, PSEN1.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"49951b41-58ce-434b-9fda-a35f099a5339","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:43.014583+00:00","summary":"","completion_summary":"Enhanced gene/protein infoboxes with external database quick-links (GeneCards, UniProt, NCBI Gene, Human Protein Atlas, STRING). Added disease infobox links (OMIM, Orphanet, ClinicalTrials.gov, PubMed). Ran backfill for 2363 pages. Existing infobox system was already comprehensive with 415-line gene/protein and 175-line disease renderers.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"54346f4e-2621-40dd-8619-2f9c3d249318","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.999196+00:00","summary":"","completion_summary":"Added structured infoboxes for cell/cell_type, mechanism, therapeutic, and pathway wiki pages. Built _build_cell_infobox (shows aliases, definition, functions, key markers as gene links, states, pathways, diseases, discovery) and _build_mechanism_infobox (shows name, category, summary, KG-derived genes/diseases/pathways, linked hypotheses with per-type styling). Wired into both /wiki/{slug} and /entity/{name} routes. Upgrades 6,330 pages from generic to structured infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7e874750-7f65-4750-9024-703e161a12f9","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.983553+00:00","summary":"","completion_summary":"Added structured infoboxes to gene/protein wiki pages: (1) Created scripts/enrich_gene_infoboxes.py that batch-enriched 4035 entities with 10600 new fields (chromosome, function, expression, protein_type, amino_acids, etc.) extracted from wiki page content and KG edges. Reduced sparse entities (<4 core fields) from 4363 to 2997. (2) Improved _build_gene_protein_infobox() rendering to filter out domain-structure table rows (signal peptide, prodomain, transmembrane domain positions) so infoboxes prioritize key summary facts.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"639846f8-52f8-48bb-b285-8d272ad972cb","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.968961+00:00","summary":"","completion_summary":"Gene/protein wiki pages already have rich infoboxes via _build_gene_protein_infobox() (Gene Symbol, Chromosome, Function, Diseases, Drugs, Interactions, UniProt/NCBI/Ensembl IDs). 7720/7720 wiki_entities have infobox_data. Added backfill script for 2374 pages with non-standard title formats. Verified TIAL1, GFAP, PARK2, LINGO1 pages all render complete infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"55bf1dcb-fcf2-4678-88f7-84001f54c0e7","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.954047+00:00","summary":"","completion_summary":"Already complete: Gene/protein wiki pages have structured infoboxes via _build_gene_protein_infobox() at api.py:16432. TREM2 example shows: Gene Symbol, Aliases, Chromosome, Protein Type, Function, MoA, Expression, Druggability, Clinical Stage, MW, AA count, Pathways, UniProt/NCBI/Ensembl IDs, Associated Diseases (linked), Known Drugs (linked), Interactions (linked), Target profile link.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"00be1c14-8668-4ee5-ac3e-f704e4b1e174","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.938773+00:00","summary":"","completion_summary":"Gene/protein/disease wiki pages already have structured infoboxes via _build_gene_protein_infobox() and _build_disease_infobox() at api.py:16432. Verified rendering: gene pages show 9+ fields (Gene Symbol, Chromosome, Function, etc.), protein pages 11-14 fields, disease pages 11+ fields. Entity pages also render infoboxes. No changes needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7cbcc430-28fa-460d-b8c5-859f2e53c303","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.923194+00:00","summary":"","completion_summary":"Already implemented. All 6,972 gene/protein wiki pages (3,866 genes + 3,106 proteins) have structured HTML infoboxes with gene symbol, full name, chromosome, protein family, function, associated diseases, known drugs. 100% coverage. Infoboxes are embedded in content_md using table.infobox class.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"956b21f9-0eee-4b29-902b-423d288dee4b","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.908282+00:00","summary":"","completion_summary":"Entity pages already have structured infoboxes with Gene Symbol, Aliases, Chromosome, Protein Type, Target Class, Function, etc. Wiki pages have infobox CSS styling. Task already satisfied.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2725d42c-f721-4116-9124-49e3958ba305","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.893691+00:00","summary":"","completion_summary":"All gene/protein wiki pages already have infoboxes (11920 pages with infobox class). No additional work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ee5c307d-000d-4842-846e-b071b53669d6","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.879567+00:00","summary":"","completion_summary":"All gene wiki pages (3866/3866) and protein wiki pages (3106/3106) already have structured infoboxes with gene symbol, function, disease associations, and drug information. CSS styling for dark mode infoboxes is also in place. 100% coverage.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3553de3c-a490-4932-9e30-712913dcbf61","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.863320+00:00","summary":"","completion_summary":"Added structured infoboxes to 852 wiki entities that were missing them. All 8,990 wiki entities now have infobox_data. Infoboxes include name, type, KG edge count, top relations breakdown, and associated diseases extracted from knowledge graph connections.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b2b083a8-3bf3-4f45-95bd-550d991d0343","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.847124+00:00","summary":"","completion_summary":"Created scripts/enrich_gene_infoboxes.py that parses wiki page content (HTML infobox tables, markdown tables, bullet lists) to extract structured gene/protein fields into wiki_entities.infobox_data. Enriched 5275 entities and created 266 new ones. Chromosome data: 3193→3675. Added NCBI Gene IDs (2176), UniProt IDs (3976). All tested wiki pages render 200 with richer infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7d642865-818c-4867-af15-b8df22035651","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.831156+00:00","summary":"","completion_summary":"Improved structured infoboxes on gene/protein wiki pages: (1) Fixed HTML table parsing to filter out sub-table rows using known-attr-key whitelist, (2) Deduplicated aliases that match Full Name, (3) Added function_summary fallback for garbled function fields, (4) Enriched mechanism/therapeutic/pathway infoboxes with KG-linked genes/diseases, (5) Added full_name and gene_symbol to infobox_data field mapping.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"82ef131a-342d-40b9-bc33-2293a9658c15","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.814624+00:00","summary":"","completion_summary":"Structured infoboxes already fully implemented on gene/protein wiki pages. TP53 example shows gene symbol, function, Ensembl ID, associated diseases, interactions, pathway diagrams. Built by _build_gene_protein_infobox() function using wiki_entities.infobox_data JSON, knowledge graph edges, and targets table for druggability data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c00f9ca2-ec6d-48a9-9389-6df36a588437","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.798916+00:00","summary":"","completion_summary":"Already implemented. All 6,972 gene/protein wiki pages have structured infoboxes with Quick Reference sections including gene symbol, chromosome, function, associated diseases, and known drugs. Infobox CSS dark-mode styling is in place. Verified on TREM2 wiki page.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"686b717c-320e-45ef-abd0-6d99a6fe8c8c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.783271+00:00","summary":"","completion_summary":"Gene/protein wiki pages already have structured infoboxes with gene symbol, chromosome, function, Uniprot IDs, and more. Verified on TREM2, APOE, Tau, LRP1 pages — all have 10+ infobox elements each.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4f92f12d-c940-4901-9000-dd3a9d342037","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.768501+00:00","summary":"","completion_summary":"Already implemented. All 6,972 gene/protein wiki pages have infobox content in their markdown. CSS styling for infoboxes in dark mode is in the wiki page renderer. Infoboxes show gene symbol, function, associated diseases, etc.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"77812fb1-6676-4ff9-a251-22b60b3ed915","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.753490+00:00","summary":"Already implemented - 7702/7720 gene/protein entities have structured infoboxes","completion_summary":"Duplicate task - already implemented. _build_gene_protein_infobox() at api.py:15525 renders structured infoboxes for all 6972 gene/protein wiki pages with gene symbol, chromosome, function, associated diseases, known drugs, and external DB links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"afacd07f-6e8a-4f1d-8bca-e523fbc4f6bc","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.738511+00:00","summary":"","completion_summary":"Already implemented: _build_gene_protein_infobox() at api.py:15525 renders structured infoboxes for all 6972 gene/protein wiki pages with gene symbol, chromosome, function, associated diseases, known drugs, protein interactions, and external DB links (UniProt, NCBI, Ensembl, OMIM). Verified BRCA1, TP53, EGFR all render correctly with rich infobox data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e7255015-68a3-4267-809a-cd76edd74ae4","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.724352+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bfdf3ce3-8771-4bbf-94db-d2d6e707f5d8","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.707360+00:00","summary":"","completion_summary":"Duplicate - already verified complete. Entity pages have structured infoboxes with gene symbol, aliases, chromosome, function, druggability, UniProt ID, diseases, drugs, interactions.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"40641dce-2bf7-4705-bb63-ad4bff3aac87","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.692864+00:00","summary":"","completion_summary":"Already complete. Entity pages have structured infoboxes with: gene symbol, aliases, chromosome, protein type, function, mechanism of action, druggability score, clinical stage, molecular weight, amino acids, exons, pathways, UniProt ID, associated diseases, known drugs/compounds, protein interactions, and SciDEX target profile links. Wiki pages also have CSS dark-mode styled infobox support.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fd167825-a5cb-4286-a98f-9bd65c969545","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.678340+00:00","summary":"","completion_summary":"Already fully implemented: _build_gene_protein_infobox() at api.py:11088 generates structured infoboxes with Gene Symbol, Full Name, Chromosome, Function, Associated Diseases (from KG), Known Drugs (from KG), and Interactions (from KG). Used on both entity detail pages and wiki pages for gene/protein entity types. Verified rendering on TREM2, MITF, ST6GALNAC5, KCNS2.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ec49eb6c-60af-445b-b070-bfae976cf7de","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.663449+00:00","summary":"","completion_summary":"Task already complete. Wiki pages already have structured infoboxes: _build_gene_protein_infobox() at line 14880 parses markdown attribute tables, enriches with KG data (diseases, drugs, interactions), wiki_entities infobox_data, and renders structured display with gene symbol, chromosome, function, associated diseases, known drugs. _build_disease_infobox() handles disease pages. Generic infobox renders frontmatter fields for other entity types. All rendered on both /wiki/{slug} and /entity/{name} pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"acc76053-34c4-449d-9c7c-ecd249e9767c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.648070+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b474be94-d5d4-46a3-a8f8-b41a009bd556","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.630899+00:00","summary":"","completion_summary":"Duplicate of 014b347b. Already implemented — all gene/protein wiki pages have structured infoboxes with gene symbol, chromosome, function, associated diseases, known drugs via _build_gene_protein_infobox() in api.py.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"014b347b-594e-438c-9e40-9702418d2abf","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.615577+00:00","summary":"","completion_summary":"Already implemented. All 3866 gene and 3106 protein pages have inline HTML infoboxes in content_md. The dynamic _build_gene_protein_infobox() function (api.py:14012-14407) enriches these at render time with KG edges (diseases, drugs, interactions), target profiles (druggability, clinical trials, mechanism), and wiki_entities data (chromosome, molecular weight, pathways, external IDs). External links to UniProt, NCBI, Ensembl, and OMIM are auto-generated. Verified TREM2 and other pages render all requested fields: gene symbol, chromosome, function, associated diseases, known drugs.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4a8d0917-1217-4746-9d17-7247f477f123","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.598218+00:00","summary":"","completion_summary":"Improved gene/protein infoboxes: added NCBI Gene alias and OMIM field with external links, filtered duplicate Disease/KG Connections rows from generic attrs, strip markdown link syntax from parsed values, deduplicate KG diseases case-insensitively","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c6bb9367-1a7f-4179-8cb8-b49775f0f8d2","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.583418+00:00","summary":"","completion_summary":"Extended wiki page infoboxes from gene/protein to 8 entity types (drug_target, receptor, enzyme, transporter, biomarker). Added new _build_disease_infobox() for 491 disease wiki pages with KG-enriched associated genes, drugs, and pathways. Also updated entity detail page to show disease infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"add89f69-745b-49d7-a79b-eeb0d031f146","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.568582+00:00","summary":"","completion_summary":"Already complete: _build_gene_protein_infobox() at api.py:13757 renders structured infoboxes for all 3866 gene and 3106 protein wiki pages. Includes gene symbol, chromosome, function, associated diseases, known drugs, interactions, druggability, clinical stage, pathways, and external DB links (UniProt, NCBI, Ensembl). Enriched from markdown content parsing, wiki_entities.infobox_data, KG edges, and targets table.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3f6df723-3a57-40ba-a0a9-c962c476e16a","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.551994+00:00","summary":"","completion_summary":"Gene/protein wiki pages already had 100% infobox coverage with basic fields (symbol, name, chromosome, NCBI/UniProt links). Enriched 4,064 pages by adding structured cross-links: Associated Diseases from KG edges, Related SciDEX Hypotheses with composite scores and links, and KG Connection counts. Total gene/protein pages with cross-links: 4,306/6,972.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"24ab7b74-7590-4d64-b0a4-580d0b485986","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.535654+00:00","summary":"","completion_summary":"Gene/protein wiki infoboxes already implemented and rendering correctly. Checked genes-trem2 and genes-apoe: structured infoboxes include gene symbol, chromosome, NCBI Gene ID, Ensembl, OMIM, UniProt, diseases, expression patterns, mutations, and protein interactions. All 3866 gene and 3106 protein pages have frontmatter data. The _build_gene_protein_infobox function in api.py generates rich infoboxes from page frontmatter. No additional work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"dfabfb48-6de8-4a35-84c3-43af1c977473","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.522024+00:00","summary":"","completion_summary":"Structured infoboxes already present on 11,920 of 17,257 wiki pages (69%). Key gene/protein pages (TREM2, APOE, APP, PSEN1, GBA1, MAPT) all have infoboxes with gene symbol, protein, chromosomal location, primary expression, risk variants, and associated diseases. Infobox styling with dark theme renders correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"25893f35-7ffb-466b-a40d-83e9e396bdc3","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.506855+00:00","summary":"","completion_summary":"Task already fully implemented. The _build_gene_protein_infobox() function in api.py (line 13369-13744) renders structured infoboxes on all 6972 gene/protein wiki pages. Infoboxes include: Gene Symbol, Full Name, Aliases, Chromosome, Function, Primary Expression, Protein Family, Pathways, UniProt/NCBI/Ensembl IDs, Associated Diseases (from KG edges), Known Drugs (from KG + targets table), Interactions, Druggability, Clinical Stage, and Mechanism of Action. Data sourced from: markdown content parsing, wiki_entities.infobox_data, knowledge_edges, and targets table. Verified 10 random pages — all render infoboxes correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7cc2f3b3-cc21-425d-8d5b-6ae5cab5aa3a","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.491716+00:00","summary":"","completion_summary":"Infoboxes already exist and render richly on gene/protein entity pages. Verified on CD33, GBA1, LRRK2 — showing Gene Symbol, Full Name, Aliases, Chromosome, Function, Molecular Weight, Amino Acids, Exons, UniProt/NCBI/Ensembl IDs, Associated Diseases, and Interactions. 8,125 out of 7,702 gene/protein entities have infobox_data. Both entity pages (/entity/) and wiki pages (/wiki/) render them.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a6d7e14a-7a4b-411a-9be1-89640cdb87a6","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.477817+00:00","summary":"","completion_summary":"Duplicate. Wiki entity pages have structured data from wiki_entities table.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"39350698-5a23-4dd1-9ab1-b2ad5e018795","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.462822+00:00","summary":"","completion_summary":"Added structured infoboxes to all 7702 gene/protein wiki entities: filled 15 completely missing, added gene_symbol to 4608 (29%→89%), enriched 143 from targets table with diseases/function/uniprot. All entity pages now render with full infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"07a5ba90-3060-4e88-b3f2-294d59574c42","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.447848+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"411442bf-f867-4d6c-9ffc-67da6369682f","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.433210+00:00","summary":"","completion_summary":"Already complete - all 6,972 non-redirect gene/protein wiki pages have structured infoboxes with gene symbols, functions, disease associations, etc. 84 redirect stubs intentionally omit infoboxes. CSS styling for dark-mode infoboxes is already in place.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"478cb58d-33e4-4ea1-903b-94a3e75fbb4f","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.418942+00:00","summary":"","completion_summary":"Fixed protein infobox ID resolution: strip PROTEIN suffix from kg_node_ids, try multiple search candidates for wiki_entities and KG edge lookups, added clickable external DB links (UniProt/NCBI/Ensembl). Coverage improved from 466 to 2928 protein pages with structured infobox data (15% -> 94%).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4e672fbb-02e5-43ee-9658-8eac50459897","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.403752+00:00","summary":"","completion_summary":"Fixed gene/protein wiki infoboxes: stripped markdown bold artifacts from parsed table keys/values, improved KG entity resolution to try multiple candidate IDs (gene symbol, kg_node_id, title-derived) and pick the first with actual edges, added Gene Symbol fallback for sparse pages. Merged with upstream enhancements (bullet-list parsing, wiki_entities.infobox_data, targets table enrichment).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"361c9ba6-0329-4779-9491-aafe659f7091","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.387335+00:00","summary":"","completion_summary":"All 7687 gene/protein wiki entities now have structured infobox data (gene symbol, chromosome, function, diseases, drugs, pathways). Enriched the final 4 missing entities: AQUAPORIN-4, GASDERMIN, C-MYC, PI3KC3. The API already renders infoboxes via _build_gene_protein_infobox(). Verified pages render correctly.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1bc8580b-5a7b-4986-9681-eb8a439f2dfc","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.372047+00:00","summary":"","completion_summary":"Gene/protein entity pages already have structured infoboxes. Verified: /entity/TREM2 (5 data fields: Category, Target, Diseases, Drugs, Interactions), /entity/APOE (6 fields), /entity/MAPT (4 fields). Wiki pages have infobox CSS with dark-mode styling. The entity page route dynamically renders structured data from KG edges, wiki links, and hypothesis connections. No additional work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5ab86567-d2d2-4182-8688-e68b4ae43841","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.357637+00:00","summary":"","completion_summary":"Enriched 5,673 gene/protein wiki entities with 12,745 structured infobox fields (gene symbol, chromosome, function, diseases, UniProt, NCBI Gene ID, Ensembl ID, etc.). Added standalone **Key:** Value pattern parsing to _build_gene_protein_infobox(). Function coverage went from 25 to 1,561 pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"41267cbd-2cb9-4593-bae4-d8e979ec10ea","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.342101+00:00","summary":"","completion_summary":"Enhanced gene/protein wiki page infoboxes with targets table integration: druggability bucket/score, clinical stage, mechanism of action, target class, known drugs from targets table, and SciDEX Target profile link with clinical trials count. Enriches 150 gene pages matching the targets table with richer drug discovery context.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"115a6883-4c8b-4b3a-aae2-0927ab16286a","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.327270+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5a31eda6-b2ae-43b9-b2c0-86aaebedd4ff","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.313006+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e9a111f9-8054-4772-adf2-93285e17917a","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.296323+00:00","summary":"","completion_summary":"Enhanced _build_gene_protein_infobox() to pull structured data from wiki_entities.infobox_data for 7,660+ gene/protein entities. Now shows chromosome, molecular weight, amino acids, exons, aliases, pathways, and disease fallbacks. Committed on branch worktree-wiki-infoboxes.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"cedabea8-e350-4cd2-828b-1afe34ffb424","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.281142+00:00","summary":"","completion_summary":"Enhanced gene/protein infobox rendering to merge pre-computed infobox_data from wiki_entities table (7,644 entities). Maps chromosome, exons, amino_acids, molecular_weight, aliases, functions, pathways, diseases into the infobox display. Provides fallback data when wiki page content lacks structured markdown tables. Branch: worktree-wiki-infobox-enrich","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6bcbfe94-ce61-46c4-9cab-44c4cd0622bf","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.265579+00:00","summary":"","completion_summary":"Already complete: gene/protein wiki pages have structured infoboxes with gene symbol, full name, chromosome, function, expression, UniProt/Ensembl/NCBI IDs, associated diseases, known drugs, and interactions. Built via _build_gene_protein_infobox() which parses content + enriches from KG. 7626/7665 gene/protein entities have infobox_data, and content parsing covers the rest.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ea17c481-4dc7-4998-8ecc-a16e83618423","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.250766+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c8e3c6c2-afe9-4dd2-adcf-e5270f27f303","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.236725+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"dfb18a99-2c1e-4e95-a8d3-49190290ee9c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.222696+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"51a4828f-30ab-4ed5-9f11-c1b442033cb6","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.208367+00:00","summary":"","completion_summary":"Already done - 7,566 entities have infoboxes. Multiple commits added infoboxes for genes, proteins, diseases, pathways.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4b180be7-3ed0-4183-9880-696836ee43e0","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.192575+00:00","summary":"","completion_summary":"Verified: Gene/protein wiki pages already have structured infoboxes. genes-trem2 shows 32 infobox elements including gene symbol, function, associated diseases, and drugs.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e562f7c8-d5dd-4c8c-afb9-1b1db93af3f7","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.176035+00:00","summary":"","completion_summary":"Already complete: _build_gene_protein_infobox function exists in api.py (24 references), infoboxes rendered on wiki pages (TREM2 page has 11 infobox elements).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"90771ad4-3d51-4b55-98e4-b1872f047385","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.158263+00:00","summary":"","completion_summary":"Duplicate task — already complete. _build_gene_protein_infobox() function exists with markdown/HTML table parsing, KG enrichment, and structured rendering. Generic infobox for non-gene entities also implemented.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"21cc3570-5aa1-403a-8d4d-fe2e91b3d505","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.140887+00:00","summary":"","completion_summary":"Enhanced _build_gene_protein_infobox to parse bullet-list format (- **Key:** Value) and extract gene symbols from titles. Added infobox to entity detail pages for gene/protein types. Covers 5300+ gene/protein pages that previously had minimal infobox data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7719bc4c-dee2-4b52-bcd9-74a8cb2cbd8c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.125371+00:00","summary":"","completion_summary":"Already implemented: _build_gene_protein_infobox() at line 10828 — parses markdown/HTML attribute tables, enriches with KG data (diseases, drugs, interactions), renders structured infobox with gene symbol, chromosome, function, expression, UniProt/NCBI IDs. Called at line 11068 for gene/protein wiki pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"87e63452-3490-43a0-b583-b3c908018f29","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.109890+00:00","summary":"","completion_summary":"Already implemented — _build_gene_protein_infobox() function exists (line 10849) that builds structured infoboxes for gene/protein wiki pages. Extracts key facts from content markdown and frontmatter (gene symbol, chromosome, function, associated diseases, known drugs). Generic infobox fallback for other entity types. Dark mode CSS styling included.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9151d905-021e-418a-91b3-f1213567b729","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.094930+00:00","summary":"","completion_summary":"Gene/protein infoboxes already fully implemented via _build_gene_protein_infobox() in api.py. Verified BRCA1 and TP53 pages render structured infoboxes with: Gene Symbol, Full Name, Chromosome, IDs (NCBI/OMIM/Ensembl/UniProt), Associated Diseases (linked), and Interactions (linked). No additional work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"07f4cb77-dada-4d5a-9a87-2083ab407d9a","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.077953+00:00","summary":"","completion_summary":"Verified: Structured infoboxes already implemented for gene/protein wiki pages via _build_gene_protein_infobox function. All 6972 gene/protein pages have data. No changes needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e25078cc-f64f-4a03-9831-7fe5c6b40690","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.060707+00:00","summary":"","completion_summary":"Added Wikipedia-style floating infoboxes to gene/protein entity pages. Shows entity type, UniProt/PDB IDs, KG edge counts, hypothesis count with top score, associated diseases/pathways/interactors from KG edges, and external links (NCBI, GeneCards, AlphaFold). Branch: worktree-add-entity-infoboxes","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"cb12ee15-35c6-46f7-90c5-4a11a1b41902","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.044379+00:00","summary":"","completion_summary":"Fixed structured infoboxes for protein wiki pages: added _derive_base_gene_symbol() to strip PROTEIN/RECEPTOR/etc suffixes from kg_node_ids for wiki_entities and KG edge lookups (matching ~2700 more protein pages). Combined KG queries with IN() for 10x speedup (5.1s -> 0.45s). Added clickable external links for UniProt, NCBI Gene, and Ensembl IDs. Branch: worktree-wiki-infoboxes-v2","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"da61bb6f-f032-49cd-9d6c-71be3fce2688","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.029516+00:00","summary":"","completion_summary":"Already implemented: _build_gene_protein_infobox() in api.py renders structured infoboxes with gene symbol, chromosome, function, associated diseases, known drugs, and interactions. Generic infoboxes also exist for non-gene/protein entity types. Verified rendering on /wiki/genes-apoe.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e95df9ef-6fe4-4e74-a206-a68ef630301a","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:42.014023+00:00","summary":"","completion_summary":"Enriched gene/protein wiki infoboxes with wiki_entities.infobox_data. Previously ~7000 pages had empty infoboxes. Now populates chromosome, molecular weight, amino acids, exons, aliases, pathways, and functions from structured entity data. Also falls back to infobox_data diseases when KG returns none.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c598ed6f-ffde-4729-943e-69f8537ed4ab","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.998085+00:00","summary":"","completion_summary":"Already implemented. _build_gene_protein_infobox() at api.py:10706-10878 renders structured infoboxes for 6972 gene/protein wiki pages with: gene symbol, chromosome, function, protein family, expression + KG-enriched diseases, drugs, interactions. Verified /wiki/mitf renders 200 with infobox content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e64d59d0-ace2-4589-9f7e-7fce6d7952df","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.982359+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"69d4b920-86a6-48ed-8daa-60a9c1b73e5c","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.967979+00:00","summary":"","completion_summary":"Enriched gene/protein wiki infoboxes: (1) Pull structured data from wiki_entities.infobox_data for 7,557 pages lacking markdown tables, (2) Fixed KG edge lookup to use gene symbols instead of entity IDs - HDAC6 now shows 176 edges vs 0 before. Branch: worktree-wiki-infoboxes-2","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fb56a7fe-69ac-490f-9c54-40071eae1bac","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.953698+00:00","summary":"","completion_summary":"Already complete. _build_gene_protein_infobox() at api.py:8353 generates structured infoboxes for gene/protein wiki pages with: Gene Symbol, Full Name, Chromosome, Protein Family, Function, Expression, Associated Diseases, Known Drugs. CSS dark-mode styles applied. Verified on /wiki/mitf and /wiki/hdac6.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"33d996dc-3895-4287-aec9-bb2a1d103232","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.939703+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4d2bae6c-7717-41b2-8274-3cdc08cc64ef","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.925760+00:00","summary":"","completion_summary":"Enhanced _build_gene_protein_infobox() to read additional fields (function_summary, full_name, protein_family, expression, uniprot_id, gene_symbol). Created backfill script that extracted structured data from 4,312 gene/protein wiki pages and stored in wiki_entities.infobox_data (total with data: 7,557).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3b819176-4455-4d4e-8f8b-f11a6fb1d8e1","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.911095+00:00","summary":"","completion_summary":"Added structured infoboxes to gene/protein wiki pages. Fixed infobox_data query that was returning empty rows. Added extraction of chromosome, molecular weight, amino acids, exons from wiki_entities structured data. Bulk-populated infobox_data for 6,101 gene/protein entities (up from 20). Branch: worktree-wiki-infoboxes","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bcd8ab0b-ee8f-43e1-b07a-3470f4c7efa6","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.","status":"archived","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:41.893760+00:00","summary":"","completion_summary":"Enhanced _build_gene_protein_infobox() to extract structured facts from prose text (chromosome, MW, amino acids, exons), frontmatter titles, wiki_entities.infobox_data (aliases, functions, pathways, diseases), and targets table (druggability, hypothesis/paper counts). Affects ~6,972 gene/protein wiki pages. Branch: worktree-wiki-infoboxes","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9cb9abc8-b15e-4791-bcb9-cef347a5d8d2","title":"[Wiki] Add structured infoboxes to gene/protein wiki pages","description":"Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:17:25.002575+00:00","updated_at":"2026-04-19T04:17:25.002575+00:00","summary":"","completion_summary":"Already resolved: gene/protein infoboxes confirmed on main via _build_gene_protein_infobox (api.py:52371), 200 verified on /wiki/genes-foxp1 and /wiki/genes-trem2","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9cb9abc8-b15_wiki_add_structured_infoboxes_to_gene_p_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: gene/protein infoboxes confirmed on main via _build_gene_protein_infobox (api.py:52371), 200 verified on /wiki/genes-foxp1 and /wiki/genes-trem2","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"860a1796-f5d4-4860-bf37-7e5b94bb9bd2","title":"[Wiki] Add mermaid diagrams to next batch of 100 wiki pages with KG edges","description":"5,209 wiki pages have mermaid diagrams. Many more pages have matching KG edges but no diagrams yet. Generate mermaid flowcharts for the next 100 most-connected wiki pages. Use slug-based matching for wiki_pages to knowledge_edges. Write directly to DB with retry logic for lock handling.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:10:01.580072+00:00","updated_at":"2026-04-19T04:10:01.580072+00:00","summary":"Verified complete by slot 1","completion_summary":"[Atlas] Mark acceptance criteria done [task:860a1796-f5d4-4860-bf37-7e5b94bb9bd2]; [Atlas] Work log: add mermaid diagrams — 20 pages updated, pushed to origin [task:860a1796-f5d4-4860-bf37-7e5b94bb9bd2]; [Atlas] Add mermaid diagrams to next batch of wiki pages via slug-based KG matching","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/860a1796_f5d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f7e08d09-1a0b-47b4-83a4-3568918cc609","title":"[Wiki] Citation enrichment: metabolomics-neurodegeneration and entities-dnl310 wiki pages (2900+ words each, 0 refs)","description":"Add substantive PubMed citations to two substantial wiki pages that have no refs_json entries:\n- metabolomics-neurodegeneration (2973 words, entity type: general)\n- entities-dnl310 (3254 words, entity type: entity)\n\nSteps for each page:\n1. Fetch page: `curl -s 'http://localhost:8000/api/wiki/{slug}'`\n2. Read content_md to identify specific factual claims\n3. For metabolomics-neurodegeneration: search for papers on metabolomics biomarkers in PD/AD/ALS using paper_cache\n4. For entities-dnl310: research DNL310 (a GBA1 activator for GD/PD) and find clinical trial papers, mechanism papers\n5. Build refs_json with 8-12 citation objects per page (title, authors, year, doi/pmid)\n6. Add inline [N] citation markers at claim locations in content_md\n7. Update both wiki_pages records\n\nAcceptance criteria:\n- metabolomics-neurodegeneration: >= 8 citations, inline markers at >= 5 locations\n- entities-dnl310: >= 8 citations, inline markers at >= 5 locations\n- All citations verified as real publications (DOI or PMID resolvable)\n- Both pages render correctly","status":"done","priority":83,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T05:58:02.339159+00:00","updated_at":"2026-04-28T05:58:02.339159+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Enriched live wiki_pages rows for metabolomics-neurodegeneration and entities-dnl310: each now has 12 DOI/PMID-backed refs_json entries, 12 inline [^N] markers, word_count > 2900, and rendered /wiki pages return HTTP 200. Git commit/push unavailable because worktree gitdir is read-only in sandbox.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c5ce7319-75c7-40c1-a8d0-7b1b8f53efcc","title":"[Wiki] Substantive content expansion: 3 thin wiki pages on cell types and mechanisms (500+ words each)","description":"Expand content for 3 thin wiki pages that have fewer than 200 words, making them substantive reference pages.\n\nTarget pages (query: `SELECT slug, title, word_count FROM wiki_pages WHERE word_count < 200 AND word_count > 0 ORDER BY word_count DESC LIMIT 10`):\n- Pick 3 from the top-10 thin pages relevant to neurodegeneration\n\nSteps for each page:\n1. Identify the entity type and subject of the page\n2. Research the topic using paper_cache and the SciDEX knowledge base\n3. Write 500-800 word content covering: definition, biological role, disease relevance, key research findings\n4. Add 5+ citations from PubMed papers\n5. Update content_md, word_count, and refs_json in wiki_pages\n\nAcceptance criteria:\n- 3 pages expanded from < 200 words to > 500 words each\n- Each page has >= 5 citations in refs_json\n- Content is scientifically accurate and relevant to neurodegeneration research\n- Pages render correctly and word_count updated","status":"done","priority":82,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T06:07:33.567580+00:00","updated_at":"2026-05-16T04:11:35.948689+00:00","summary":"","completion_summary":"Task complete. Expanded 3 thin neurodegeneration wiki pages via direct PostgreSQL writes:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Legacy done-evidence audit backfill: task was already marked done with an already-resolved/no-merge/shipped summary. Original summary: Task complete. Expanded 3 thin neurodegeneration wiki pages via direct PostgreSQL writes:","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9bb2c2a5-3ffb-4c6b-b4e7-74a454af7e51","title":"[Wiki] Citation enrichment: cell-types-medium-spiny-neurons-huntington and ideas-payload-msa-combination-therapy (3000+ words each, 0 refs)","description":"Add PubMed citations to two substantial wiki pages with 3000+ words but empty refs_json:\n- cell-types-medium-spiny-neurons-huntington-disease (3029 words)\n- ideas-payload-msa-combination-therapy (3049 words)\n\nSteps for each page:\n1. Fetch content: `curl -s 'http://localhost:8000/api/wiki/{slug}'`\n2. Identify 8+ specific claims needing citation\n3. For medium spiny neurons in HD: search for striatal neuron degeneration, DARPP-32, CAG repeat toxicity papers\n4. For MSA combination therapy: search for multiple system atrophy treatment, synuclein+autonomic papers, combination therapy approaches\n5. Build refs_json with real PubMed citations (PMID/DOI)\n6. Add inline [N] markers in content_md\n7. Update both wiki pages\n\nAcceptance criteria:\n- Both pages have >= 8 citations in refs_json\n- At least 6 inline citation markers per page\n- Citations are scientifically relevant and from peer-reviewed journals\n- Both pages render correctly","status":"done","priority":82,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T06:11:12.068657+00:00","updated_at":"2026-04-28T06:11:12.068657+00:00","summary":"","completion_summary":"[Atlas] Add 8 PubMed citations each to MSN/HD and MSA combo therapy wiki pages [task:9bb2c2a5-3ffb-4c6b-b4e7-74a454af7e51]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Enriched 2 wiki pages (3000+ words each, 0 refs) with 8 citations each via PubMed search + inline [PMID:] markers: cell-types-medium-spiny-neurons-huntington-disease (8 PMIDs covering MSN vulnerability mechanisms) and ideas-payload-msa-combination-therapy (8 PMIDs covering MSA tripartite pathophysiology). Both pages now render with 8 refs_json entries and 8 inline markers. Committed e94017da2 to task branch.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c6ca2d7d-fedd-4e30-9f52-65f082a6ccf3","title":"[Atlas] Link 50 wiki pages to canonical entity identifiers","description":"17232 wiki pages lack canonical_entity_id values, so entity pages cannot unify all Atlas knowledge.\n\n## Acceptance criteria\n\n- 50 wiki pages gain canonical_entity_id values matched to existing KG entities\n- Ambiguous pages are left unchanged with documented no-link rationale rather than guessed\n- Remaining wiki pages missing canonical_entity_id is <= 17182\n\n## Approach\n\n1. Select high-traffic or entity-like wiki pages missing canonical_entity_id.\n2. Match against existing KG entities using title, slug, kg_node_id, and refs context.\n3. Persist only high-confidence canonical links and verify entity pages aggregate them.\n\nGenerated by the quest-engine low-queue cycle after live DB gap verification. Re-check for duplicate recent work before editing, and document any stronger framing you find.\n","status":"done","priority":82,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T01:56:41.700597+00:00","updated_at":"2026-04-28T01:56:41.700597+00:00","summary":"","completion_summary":"[Atlas] Link 50 wiki pages to canonical KG entities [task:c6ca2d7d-fedd-4e30-9f52-65f082a6ccf3]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_engine_wiki_kg_node_linking_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6}, \"completion_shas\": [\"b7e3f97a1\"], \"completion_shas_checked_at\": \"\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"DB updated via 5192f3b27. canonical_entity_id count 17232 → 17182. 50 pages mapped. Verified: /api/wiki/genes-abca2 -> ABCA2, /entity/ABCA2 -> HTTP 200. Diff vs origin/main: only spec work log (63 lines).","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9f80cb3b-c98f-4edc-9322-22eca4e58c50","title":"[Wiki] Add mermaid diagrams to next batch of high-connectivity entities","description":"Generate mermaid pathway/relationship diagrams for top-connected wiki entities that don't have them yet. Target: 50+ entities.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T05:22:00.967326+00:00","updated_at":"2026-04-19T05:22:00.967326+00:00","summary":"","completion_summary":"Already addressed: mermaid diagrams cover 14,041/14,043 wiki entities (99.99%). Zero entities without mermaid that also have 3+ KG edges. Commits f8904f28e and ddd2b03fb land the fix.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9f80cb3b_c98_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}, \"completion_shas\": [\"cb945b20c\"], \"completion_shas_checked_at\": \"2026-04-16T22:55:12.945058+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"397ff5fb-0e5e-4e66-897b-c8981e84b499","title":"[Wiki] Mermaid diagram generation: add pathway diagrams to 5 mechanism wiki pages lacking visual content","description":"Generate and embed Mermaid pathway diagrams into 5 mechanism wiki pages that currently lack visual content.\n\nTarget mechanism pages (select from wiki_pages WHERE entity_type='mechanism' AND content_md NOT LIKE '%mermaid%' AND word_count > 500):\n- mechanisms-ion-channel-dysfunction-disease-comparison\n- mechanisms-lysosomal-pathway-dysfunction (if exists, else another)\n- mechanisms-mitochondrial-dynamics\n- mechanisms-neuroinflammation-cascade\n- mechanisms-protein-aggregation (or nearest match)\n\nSteps for each page:\n1. Read content_md to understand the mechanism\n2. Design a Mermaid flowchart showing the key molecular steps\n3. Validate the Mermaid syntax (no syntax errors)\n4. Embed the diagram code block in content_md at an appropriate location\n5. Update the wiki page record\n\nAcceptance criteria:\n- 5 mechanism pages have Mermaid diagram code blocks added\n- Each diagram has >= 5 nodes showing the mechanistic pathway\n- Mermaid syntax is valid (parseable)\n- Pages render correctly with the embedded diagrams\n- Diagrams are scientifically accurate to the page content","status":"done","priority":81,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T06:13:00.574291+00:00","updated_at":"2026-05-16T04:11:35.948689+00:00","summary":"","completion_summary":"Successfully completed the task. Here's a summary:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Legacy done-evidence audit backfill: task was already marked done with an already-resolved/no-merge/shipped summary. Original summary: Successfully completed the task. Here's a summary:","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c14f691d-665d-443f-a25a-d43bd2dfd3fb","title":"[Wiki] Expand 10 stub wiki pages to 500+ words (297/17399 are stubs)","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n297 wiki pages have <200 words. Expand with descriptions, related entities, references.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":78,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T10:51:28.167770+00:00","updated_at":"2026-04-19T10:51:28.167770+00:00","summary":"","completion_summary":"Auto-completed by abandonment watchdog: 557 commit(s) on orchestra/task/c14f691d-expand-10-stub-wiki-pages-to-500-words-2","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8d1469e2-4482-4a36-b89f-f1a0080c2aa2","title":"[Wiki] Expand 10 stub wiki pages to 500+ words (254/17333 are stubs)","description":"254 wiki pages have <200 words. Expand with descriptions, related entities, references.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":78,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T10:38:51.128134+00:00","updated_at":"2026-04-19T10:38:51.128134+00:00","summary":"","completion_summary":"Blocked: scidex.db B-tree corruption prevents wiki stub expansion","completion_notes":"Cannot complete: scidex.db has B-tree corruption (sqlite error 11) and is locked by 3 running processes (PIDs 1125296, 1142974, 1159718). The expand_stubs.py script exists with correct logic, and prior work (commits b9d7008e2, 360a81a78) expanded 11 stubs but those commits are on orphan branches, not main. DB repair/escalation to operators needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"069264cf-e37e-4c7b-af99-0c314fc52de2","title":"[Wiki] Add structured infoboxes to 10 gene/protein entity pages","description":"52 wiki entities lack infoboxes. Add gene symbol, function, associated diseases, known drugs.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":75,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T11:18:13.071669+00:00","updated_at":"2026-04-19T11:18:13.071669+00:00","summary":"","completion_summary":"Cannot execute: production DB /home/ubuntu/scidex/scidex.db is corrupted (sqlite error 11: \"database disk image is malformed\"). The infobox enrichment scripts (enrich_wiki_infoboxes.py, enrich_all_infoboxes.py) already exist in main and would handle this task, but they require a readable DB to run. Escalating for DB restoration before infobox work can proceed.","completion_notes":"DB corruption evidence: sqlite3 returns \"database disk image is malformed\". The infobox enrichment scripts exist in main at enrichment/enrich_wiki_infoboxes.py and enrichment/enrich_all_infoboxes.py - these would handle adding structured infoboxes (gene_symbol, function_summary, diseases, known_drugs) to gene/protein wiki_entities. But they read/write wiki_entities and knowledge_edges tables which are unreadable due to DB corruption. DB file size: 2.8GB with valid WAL (32768 bytes shm, 0 bytes wal) suggesting mid-write corruption. Requires DB restore from backup before infobox enrichment scripts can be executed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0d37548c-12fe-4d8e-9f71-08504ce3bf89","title":"[Wiki] Add structured infoboxes to 10 gene/protein entity pages","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n42 wiki entities lack infoboxes. Add gene symbol, function, associated diseases, known drugs.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":75,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T11:18:03.561276+00:00","updated_at":"2026-04-19T11:18:03.561276+00:00","summary":"","completion_summary":"Already resolved: 4e3098835. Gene/protein infoboxes implemented via _build_gene_protein_infobox in api.py (line 52699+), all 13640 entities have structured infobox_data.","completion_notes":"Branch identical to main. Commit 4e3098835 already implemented gene/protein infoboxes via _build_gene_protein_infobox in api.py (line 52699+). All 13,640 wiki entities have infobox_data per prior work under task 0d37548c. No new changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"4e3098835\"], \"completion_shas_checked_at\": \"2026-04-19T11:18:03.535380+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Confirmed _build_gene_protein_infobox exists at api.py:52699 with full feature set (Gene Symbol, Full Name, Aliases, Chromosome, Function, Druggability, KG-enriched diseases/drugs, etc.). Commit 4e3098835 applied infoboxes to all 32 missing entities. Branch is identical to main with zero diff.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2235a3e1-2a74-43f4-91c3-c7111ce2497a","title":"[Wiki] Add inline citations to 40 wiki pages missing refs_json entries","description":"1,602 wiki pages have empty refs_json. For each of 40 wiki pages: (1) query paper_corpus_cache for papers relevant to the page title/entity, (2) select the 3-5 most relevant papers by relevance to the entity's neurodegenerative context, (3) populate refs_json with DOI/PMID/title/authors/year fields. Focus on gene and pathway entity pages. Acceptance: 40 pages updated with refs_json containing at least 3 citations each.","status":"done","priority":72,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T15:03:24.628899+00:00","updated_at":"2026-04-26T15:03:24.628899+00:00","summary":"","completion_summary":"[Atlas] Add inline citations to 40 wiki pages missing refs_json [task:2235a3e1-2a74-43f4-91c3-c7111ce2497a]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"283d27b6-507e-4b31-a16f-55ccc2d49543","title":"[Wiki] Link 30 wiki pages to KG nodes via canonical_entity_id resolution","description":"653 wiki pages have kg_node_id = NULL. For each of 30 pages: (1) search canonical_entities by gene_symbol or entity name matching the wiki page title/slug, (2) if a match is found, set kg_node_id and canonical_entity_id on the wiki_pages row, (3) verify the link by checking that the entity has a corresponding kg_edges entry. Prioritize gene/protein entity pages. Acceptance: 30 wiki pages updated with valid kg_node_id references verified against existing KG nodes.","status":"done","priority":68,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T14:59:26.828587+00:00","updated_at":"2026-04-26T14:59:26.828587+00:00","summary":"","completion_summary":"[Atlas] Link 108 gene wiki pages to KG nodes via canonical_entity_id [task:283d27b6-507e-4b31-a16f-55ccc2d49543]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0c0c2bac-ff53-4866-91a0-3f629d508d3f","title":"[Wiki] Generate cross-links between 25 gene wiki pages and related disease pages","description":"Many wiki gene entity pages don't cross-link to the disease pages where those genes are implicated. For 25 gene entity pages: (1) identify disease associations from kg_edges (relationship types like 'associated_with', 'implicated_in'), (2) add cross-link markdown in content_md pointing to the disease wiki pages, (3) add the linked page slugs to refs_json or a links section in frontmatter_json. Focus on genes with confirmed Alzheimer's/Parkinson's/ALS associations. Acceptance: 25 gene pages updated with 2+ disease cross-links each.","status":"done","priority":65,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T15:00:22.572374+00:00","updated_at":"2026-04-26T15:00:22.572374+00:00","summary":"","completion_summary":"[Atlas] Add gene-disease cross-link enrichment script for 25 neurodegeneration genes [task:0c0c2bac-ff53-4866-91a0-3f629d508d3f]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]}],"reviews":[],"effectiveness":{},"prs":[],"commits":[{"hash":"a220d1009","message":"[Wiki] Update spec work log after BCL2L10 fix","date":"2026-04-11"},{"hash":"fc05f82b0","message":"[Wiki] Fix BCL2L10 placeholder mermaid diagram, update spec","date":"2026-04-11"},{"hash":"a38b54251","message":"[Wiki] CI: Add mermaid diagrams to next 5 entity pages [task:c4a9a7ae-4d96-480a-9b3b-779b18ffd514]","date":"2026-04-11"},{"hash":"3593eed44","message":"[Wiki] Update spec work log — confirm task already complete [task:e9a111f9-8054-4772-adf2-93285e17917a]","date":"2026-04-10"},{"hash":"24e01bbfa","message":"[Wiki] Fix wiki_entities mermaid diagrams: 55% -> 78% valid [task:d6a62b0c-d606-4390-bc38-7118f9201ddb]","date":"2026-04-07"},{"hash":"25b4468e1","message":"[Wiki] Commit utility scripts; task complete: 100% mermaid + infobox coverage [task:d6a62b0c-d606-4390-bc38-7118f9201ddb]","date":"2026-04-07"},{"hash":"498df2bcf","message":"[Wiki] Apply pass 2 mermaid fixes: 98.7% validity (17,173/17,399 pages) [task:d6a62b0c-d606-4390-bc38-7118f9201ddb]","date":"2026-04-07"},{"hash":"0b0bb3f53","message":"[Wiki] Update spec: 98% mermaid diagram validity after quality pass [task:d6a62b0c-d606-4390-bc38-7118f9201ddb]","date":"2026-04-07"},{"hash":"977766818","message":"[Wiki] Fix 1,531+ broken mermaid diagrams with regex-based validator [task:d6a62b0c-d606-4390-bc38-7118f9201ddb]","date":"2026-04-07"},{"hash":"15f763db4","message":"[Wiki] Add add_mermaid_no_kg.py script for content-based mermaid generation [task:d6a62b0c-d606-4390-bc38-7118f9201ddb]","date":"2026-04-07"},{"hash":"53e441a80","message":"[Wiki] Achieve 100% mermaid diagram coverage (17,399/17,399 pages) [task:d6a62b0c-d606-4390-bc38-7118f9201ddb]","date":"2026-04-07"},{"hash":"da2353923","message":"[Wiki] CI: MILESTONE - 100% mermaid coverage reached (17399/17399 pages) [task:d2123aa1-62db-4b2c-a0e3-ea80389fff06]","date":"2026-04-07"},{"hash":"4bd13ca8c","message":"[Wiki] CI: Add mermaid diagrams to 60 pages (AI tools/biomarkers/therapeutics); 14401/17399 pages (82.8%) [task:d2123aa1-62db-4b2c-a0e3-ea80389fff06]","date":"2026-04-07"},{"hash":"f4f87890a","message":"[Wiki] CI: Add mermaid diagrams to 40 therapeutic pages (RNA/ROCK/CBS-PSP sections); 14237/17399 pages (81.8%) [task:d2123aa1-62db-4b2c-a0e3-ea80389fff06]","date":"2026-04-07"},{"hash":"edd66f07c","message":"[Wiki] CI: Add mermaid diagrams to 25 therapeutic pages (nilotinib/NLRP3/PARP/PD); 14151/17399 pages (81.3%) [task:d2123aa1-62db-4b2c-a0e3-ea80389fff06]","date":"2026-04-07"},{"hash":"1bf6df21d","message":"[Wiki] CI: Add mermaid diagrams to 15 therapeutic pages (miRNA/mitochondrial/mTOR); 14088/17399 pages (81.0%) [task:d2123aa1-62db-4b2c-a0e3-ea80389fff06]","date":"2026-04-07"},{"hash":"5984763ce","message":"[Wiki] CI: Add mermaid diagrams to 5 therapeutic pages (IRE1/IVIG/JNK/ketogenic); 14040/17399 pages (80.7%) [task:d2123aa1-62db-4b2c-a0e3-ea80389fff06]","date":"2026-04-07"},{"hash":"93f61f0cd","message":"[Wiki] CI: Add mermaid diagrams to 5 therapeutic pages (exosome/exercise/Fabry); 13991/17399 pages (80.4%) [task:d2123aa1-62db-4b2c-a0e3-ea80389fff06]","date":"2026-04-07"},{"hash":"83d1200ff","message":"[Wiki] CI: Add mermaid diagrams to 5 protein pages (XRCC4/5/6/7/YAP1); 13812/17399 pages (79.4%) [task:d2123aa1-62db-4b2c-a0e3-ea80389fff06]","date":"2026-04-07"},{"hash":"c86f4e820","message":"[Wiki] CI: Add mermaid diagrams to 5 protein pages (SMAD6/7/9/SMARCA2/SMN); 13459/17399 pages (77.4%) [task:d2123aa1-62db-4b2c-a0e3-ea80389fff06]","date":"2026-04-07"}],"spec_content":"---\ntitle: \"Quest: Wiki\"\ndescription: \"SciDEX world model — rich wiki pages with inline citations, mermaid diagrams, infoboxes, and cross-links to the knowledge graph\"\ntype: quest\nlayer: Atlas\npriority: 85\nstatus: active\nquest_id: 58230ac8-c32\nspec_path: docs/planning/specs/quest_wiki_spec.md\n---\n\n# Quest: Wiki\n\n**Layer:** Atlas \n**Priority:** P85 (raised from P75 — inline citations now primary focus) \n**Status:** active\n\n## Vision\n\nSciDEX wiki pages are the human-readable face of the knowledge graph. The target state: every factual claim is inline-cited with a hoverable popover showing the supporting paper's title, key claim, and a quoted excerpt. Pages are structurally complete (infoboxes, mermaid diagrams, cross-links) and continuously improved by background agents.\n\nFOXP1 and FOXP2 are the current pilot focus: demonstrating best-practice inline citation, paralog cross-referencing, and speech/language disorder representation.\n\n## Current Tracks\n\n### Track A: Inline Citations (P85 — Primary)\nSee full spec: `docs/planning/specs/quest_wiki_citations_spec.md`\n\n- Rich hover popovers with claim + excerpt + figure reference\n- FOXP1 and FOXP2 pilot pages fully cited (≥8 inline citations each)\n- Recurring citation enrichment task (every 6h)\n- Paper-to-wiki backlink governance (every 12h)\n- Citation coverage report (daily)\n\n### Track B: Structural Quality (P82 — Ongoing)\n\n- Structured infoboxes on all gene/protein/disease pages\n- Mermaid pathway diagrams on mechanism pages\n- H1 headings present on all pages\n- No boilerplate \"Background\" / \"The study of X has evolved...\" filler sections\n\n### Track C: Cross-links (P78 — Ongoing)\n\n- All pages linked to related hypotheses via artifact_links\n- All pages linked to supporting analyses\n- Paralog/homolog see-also links (e.g. FOXP1 ↔ FOXP2)\n- Disease pages link to gene pages and vice versa\n\n### Track D: SciDEX Rebrand (P70)\n\nReplace all \"NeuroWiki\" references with \"SciDEX Wiki\":\n- quest_wiki_spec.md (this file — done)\n- specs: 22c4c017, 48c44e67, a7e9909f, 6391cf49 (mark as legacy)\n- api.py: HTML comments, footer text, CSS class names\n- wiki_pages.source_repo UI label\n\n## Open Tasks\n\n- [ ] [Atlas] Rich hover popover for wiki citations — claim + excerpt + figure_ref (P88)\n- [ ] [Atlas] FOXP1 page: rewrite with ≥8 inline citations, speech/language featured (P86)\n- [ ] [Atlas] FOXP2 page: rewrite with ≥8 inline citations, all disease associations cited (P85)\n- [ ] [Atlas] Create recurring wiki-citation-enrichment task (every 6h) (P82)\n- [ ] [Atlas] Create paper-to-wiki-backlink governance task (every 12h) (P80)\n- [ ] [Atlas] Add wiki_citations table migration (P75)\n- [ ] [Wiki] Add structured infoboxes to gene/protein wiki pages (P82)\n- [ ] [Wiki] CI: Add mermaid diagrams to next 5 entity pages (P78)\n- [ ] [Atlas] Replace NeuroWiki references with SciDEX in UI-facing code (P70)\n\n## Success Criteria\n\n- [ ] FOXP1 and FOXP2 pages have ≥8 inline citations each, speech/language role prominently featured\n- [ ] Hover popovers show full citation context (claim, excerpt, figure)\n- [ ] Citation coverage ≥80% for pages with linked papers\n- [ ] Recurring enrichment task runs and adds ≥5 citations per 6h pass\n- [ ] Zero \"NeuroWiki\" in active UI-facing code\n- [ ] All gene/protein pages have structured infoboxes\n\n## Work Log\n\n### 2026-04-09 — Quest Refresh\n\n- Elevated priority to P85 based on user feedback: inline citations are the #1 missing feature\n- Added inline citation quest spec (quest_wiki_citations_spec.md)\n- Identified FOXP1/FOXP2 as pilot pages — both have refs_json but zero inline markers\n- Tooltip currently shows only `authors (year)` — upgrading to rich popover with claim/excerpt\n- Renamed \"NeuroWiki\" → \"SciDEX Wiki\" throughout this spec\n- Added 4 governance/recurring task patterns for continuous citation improvement\n","spec_html":"

Quest: Wiki

Layer: Atlas \nPriority: P85 (raised from P75 — inline citations now primary focus) \nStatus: active

Vision

SciDEX wiki pages are the human-readable face of the knowledge graph. The target state: every factual claim is inline-cited with a hoverable popover showing the supporting paper's title, key claim, and a quoted excerpt. Pages are structurally complete (infoboxes, mermaid diagrams, cross-links) and continuously improved by background agents.

FOXP1 and FOXP2 are the current pilot focus: demonstrating best-practice inline citation, paralog cross-referencing, and speech/language disorder representation.

Current Tracks

Track A: Inline Citations (P85 — Primary)

\nSee full spec: docs/planning/specs/quest_wiki_citations_spec.md

  • Rich hover popovers with claim + excerpt + figure reference
    • \n
  • FOXP1 and FOXP2 pilot pages fully cited (≥8 inline citations each)
    • \n
  • Recurring citation enrichment task (every 6h)
    • \n
  • Paper-to-wiki backlink governance (every 12h)
    • \n
  • Citation coverage report (daily)
    • \n
\n

Track B: Structural Quality (P82 — Ongoing)

  • Structured infoboxes on all gene/protein/disease pages
    • \n
  • Mermaid pathway diagrams on mechanism pages
    • \n
  • H1 headings present on all pages
    • \n
  • No boilerplate "Background" / "The study of X has evolved..." filler sections
    • \n
\n

Track C: Cross-links (P78 — Ongoing)

  • All pages linked to related hypotheses via artifact_links
    • \n
  • All pages linked to supporting analyses
    • \n
  • Paralog/homolog see-also links (e.g. FOXP1 ↔ FOXP2)
    • \n
  • Disease pages link to gene pages and vice versa
    • \n
\n

Track D: SciDEX Rebrand (P70)

Replace all "NeuroWiki" references with "SciDEX Wiki":\n

  • quest_wiki_spec.md (this file — done)
    • \n
  • specs: 22c4c017, 48c44e67, a7e9909f, 6391cf49 (mark as legacy)
    • \n
  • api.py: HTML comments, footer text, CSS class names
    • \n
  • wiki_pages.source_repo UI label
    • \n
\n

Open Tasks

☐ [Atlas] Rich hover popover for wiki citations — claim + excerpt + figure_ref (P88)
\n
☐ [Atlas] FOXP1 page: rewrite with ≥8 inline citations, speech/language featured (P86)
\n
☐ [Atlas] FOXP2 page: rewrite with ≥8 inline citations, all disease associations cited (P85)
\n
☐ [Atlas] Create recurring wiki-citation-enrichment task (every 6h) (P82)
\n
☐ [Atlas] Create paper-to-wiki-backlink governance task (every 12h) (P80)
\n
☐ [Atlas] Add wiki_citations table migration (P75)
\n
☐ [Wiki] Add structured infoboxes to gene/protein wiki pages (P82)
\n
☐ [Wiki] CI: Add mermaid diagrams to next 5 entity pages (P78)
\n
☐ [Atlas] Replace NeuroWiki references with SciDEX in UI-facing code (P70)

Success Criteria

☐ FOXP1 and FOXP2 pages have ≥8 inline citations each, speech/language role prominently featured
\n
☐ Hover popovers show full citation context (claim, excerpt, figure)
\n
☐ Citation coverage ≥80% for pages with linked papers
\n
☐ Recurring enrichment task runs and adds ≥5 citations per 6h pass
\n
☐ Zero "NeuroWiki" in active UI-facing code
\n
☐ All gene/protein pages have structured infoboxes

Work Log

2026-04-09 — Quest Refresh

  • Elevated priority to P85 based on user feedback: inline citations are the #1 missing feature
    • \n
  • Added inline citation quest spec (quest_wiki_citations_spec.md)
    • \n
  • Identified FOXP1/FOXP2 as pilot pages — both have refs_json but zero inline markers
    • \n
  • Tooltip currently shows only authors (year) — upgrading to rich popover with claim/excerpt
    • \n
  • Renamed "NeuroWiki" → "SciDEX Wiki" throughout this spec
    • \n
  • Added 4 governance/recurring task patterns for continuous citation improvement
    • \n

","spec_file":"quest_wiki_spec.md"}