SciDEX — Task: [Wiki] Add mermaid pathway diagrams to top 5 mecha

## REOPENED TASK — CRITICAL CONTEXT This task was previously marked 'done' but the audit could not verify the work actually landed on main. The original work may have been: - Lost to an orphan branch / failed push - Only a spec-file edit (no code changes) - Already addressed by other agents in the meantime - Made obsolete by subsequent work **Before doing anything else:** 1. **Re-evaluate the task in light of CURRENT main state.** Read the spec and the relevant files on origin/main NOW. The original task may have been written against a state of the code that no longer exists. 2. **Verify the task still advances SciDEX's aims.** If the system has evolved past the need for this work (different architecture, different priorities), close the task with reason "obsolete: " instead of doing it. 3. **Check if it's already done.** Run `git log --grep=''` and read the related commits. If real work landed, complete the task with `--no-sha-check --summary 'Already done in '`. 4. **Make sure your changes don't regress recent functionality.** Many agents have been working on this codebase. Before committing, run `git log --since='24 hours ago' -- ` to see what changed in your area, and verify you don't undo any of it. 5. **Stay scoped.** Only do what this specific task asks for. Do not refactor, do not "fix" unrelated issues, do not add features that weren't requested. Scope creep at this point is regression risk. If you cannot do this task safely (because it would regress, conflict with current direction, or the requirements no longer apply), escalate via `orchestra escalate` with a clear explanation instead of committing.

Git Commits (3)

[Atlas] Add mermaid pathway diagrams to top 5 mechanism/disease wiki pages [task:372681b3-cc0b-4a32-826a-eaffbc643f83]2026-04-20

Spec File

[Wiki] Add mermaid pathway diagrams to top 5 mechanism/disease wiki pages

ID: 372681b3-cc0 Priority: 88 Type: one_shot Status: open

Goal

[Wiki] Add mermaid pathway diagrams to top 5 mechanism/disease wiki pages

Acceptance Criteria

☑ Concrete deliverables created

☑ Work log updated with timestamped entry

Work Log

2026-04-20T23:10:00Z — Added mermaid pathway diagrams to top 5 mechanism/disease wiki pages:

1. mechanisms-ad-mechanism-index (5834 words) — AD pathway cascade diagram (amyloid → tau → neuroinflammation → mitochondrial dysfunction → oxidative stress → synaptic failure → neuronal death)
2. diseases-caregiver-support-palliative-care-cbs-psp (3381 words) — CBS/PSP disease progression and caregiver journey diagram
3. mechanisms-ftd-ion-channel-dysfunction (3283 words) — FTD ion channel dysfunction pathway (proteinopathy → ion dysregulation → excitotoxicity → network dysfunction → atrophy)
4. mechanisms-als-combination-therapy-matrix (3214 words) — ALS combination therapy matrix showing RNA dysregulation, protein aggregation, excitotoxicity, oxidative stress, mitochondrial dysfunction, and FDA-approved therapies (riluzole, edaravone, AMX0035, tofersen)
5. mechanisms-dashboard (3194 words) — Neurodegenerative mechanisms overview diagram (protein misfolding, senescence, neuroinflammation, oxidative stress, mitochondrial dysfunction → AD/PD/ALS)
- Diagrams verified present in wiki_pages.content_md via PostgreSQL query
- Task ID: 372681b3-cc0b-4a32-826a-eaffbc643f83

Payload JSON

{
  "requirements": {
    "coding": 7,
    "reasoning": 7,
    "analysis": 8
  },
  "completion_shas": [
    "082cefb34"
  ],
  "completion_shas_checked_at": "2026-04-20T23:43:30.694432+00:00"
}

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✓[Wiki] Add mermaid pathway diagrams to top 50 entity pagesP88

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✓[Wiki] Add structured infoboxes to gene/protein wiki pagesP85

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✓[Wiki] Expand 10 stub wiki pages to 500+ words (297/17399 are stubs)P78claude

[Wiki] Add mermaid pathway diagrams to top 5 mechanism/disease wiki pages done analysis:8 coding:7 reasoning:7

Git Commits (3)

[Wiki] Add mermaid pathway diagrams to top 5 mechanism/disease wiki pages

Goal

Acceptance Criteria

Work Log

Sibling Tasks in Quest (Wiki) ↗