{"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":"036d0bab-05bb-449c-8ff5-e30548e80911","title":"[Wiki] Add mermaid pathway diagrams to top 50 entity pages","description":"Only 20 wiki entities have mermaid diagrams. 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Test: TREM2, APOE, alzheimers-disease, tau-propagation, microglia, neuroinflammation, alpha-synuclein, autophagy, blood-brain-barrier, glymphatic-system.","status":"open","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:17.994393+00:00","summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"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":"open","priority":65,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-25T07:47:18.341493+00:00","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":"{}"},{"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,"task_type":"one_shot","frequency":"","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_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\"}"},{"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. 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Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.344312+00:00","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":"{}"},{"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. 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Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.273267+00:00","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":"{}"},{"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. 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Create pathway/mechanism diagrams for the 50 most-connected entities in the KG.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.243944+00:00","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":"{}"},{"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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.228668+00:00","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":"{}"},{"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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.215315+00:00","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":"{}"},{"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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.202525+00:00","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":"{}"},{"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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.188171+00:00","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":"{}"},{"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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:39.174065+00:00","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":"{}"},{"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,"task_type":"one_shot","frequency":"","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_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\"}"},{"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,"task_type":"one_shot","frequency":"","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_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\"}"},{"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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-04T05:26:49.678017+00:00","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":"{}"},{"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 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'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:42:44.582382+00:00","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":"{}"},{"id":"a172770f-b497-4804-af4e-ac7dff680a44","title":"[Wiki] Add structured infoboxes to gene/protein wiki 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'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"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,"task_type":"one_shot","frequency":"","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_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\"}"},{"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,"task_type":"one_shot","frequency":"","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_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\"}"},{"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,"task_type":"one_shot","frequency":"","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_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. 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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,"task_type":"one_shot","frequency":"","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_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\"}"},{"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,"task_type":"one_shot","frequency":"","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_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\"}"},{"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,"task_type":"one_shot","frequency":"","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_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\"}"},{"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,"task_type":"one_shot","frequency":"","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_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\"}"},{"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":"blocked","priority":73,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-22T20:10:53.686636+00:00","updated_at":"2026-04-24T13:13:26.263738+00:00","summary":"","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/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\"}"}],"reviews":[],"effectiveness":{},"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)
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☐ [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
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☐ 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

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