SciDEX — Task: [Wiki] Add structured infoboxes to gene/protein wi

Gene and protein wiki pages should have structured infoboxes with key facts: gene symbol, chromosome, function, associated diseases, known drugs. ## 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 (1)

Squash merge: orchestra/task/9cb9abc8-add-structured-infoboxes-to-gene-protein (1 commits)2026-04-16

Spec File

[Wiki] Add structured infoboxes to gene/protein wiki pages

Quest: Wiki Priority: P85 Status: open

Goal

Add structured infoboxes to gene/protein wiki pages

Context

This task is part of the Wiki quest (Atlas layer). It contributes to the broader goal of building out SciDEX's atlas capabilities.

Acceptance Criteria

☑ Implementation complete and tested

☑ All affected pages load (200 status)

☑ Work visible on the website frontend

☑ No broken links introduced

☑ Code follows existing patterns

Approach

Read relevant source files to understand current state

Plan implementation based on existing architecture

Implement changes

Test affected pages with curl

Commit with descriptive message and push

Work Log

2026-04-16 verification — Task 9cb9abc8

Verified gene/protein infoboxes already implemented on main
_build_gene_protein_infobox exists in api.py (line 47769+) with full feature set:

- Gene Symbol, Full Name, Aliases, Chromosome, Protein Family, Protein Type
- Function, Mechanism of Action, Expression, Subcellular Localization
- Druggability, Clinical Stage, external IDs (UniProt, NCBI, Ensembl, OMIM)
- KG-enriched diseases, drugs, interactions

Enrichment code in enrichment/enrich_all_infoboxes.py and enrichment/enrich_gene_infoboxes.py
Work done under task IDs d6a62b0c / 0d37548c (commit 4e3098835)
Branch is identical to main — no new changes needed
Status: Already complete on main, closing task

2026-04-06 20:45 UTC — Task d6a62b0c

Found 32 wiki_entities with null/empty infobox_data
Discovered case-duplicate entities (e.g., lysosome vs LYSOSOME) where uppercase had data, lowercase didn't
Applied infoboxes to all 32 missing entities using data from add_wiki_infoboxes3.py
Used exact entity_name matching to avoid writing to already-populated uppercase duplicates
Final state: 0 entities missing infoboxes, 13,640/13,640 have infobox_data
Tested: /wiki/lysosome, /wiki/hippocampus, /wiki/huntingtons-disease, /wiki/endoplasmic-reticulum → all 200
Result: Done — all 32 remaining wiki entities now have structured infoboxes

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"
}