SciDEX — Task: [Atlas] Add infoboxes to top 20 most-connected wik

536 wiki entities lack infobox_data. Add structured infoboxes (JSON with type, description, key properties) to the 20 most-connected entities that don't have one yet. ## 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 (2)

[Verify] Add infoboxes to top 20 most-connected wiki entities — already resolved [task:466d13f2-ec31-44b6-8230-20eb239b6b3a]2026-04-21

Squash merge: orchestra/task/466d13f2-add-infoboxes-to-top-20-most-connected-w (1 commits)2026-04-16

Spec File

Spec: Add infoboxes to top 20 most-connected wiki entities

> ## Continuous-process anchor
>
> This spec describes an instance of one of the retired-script themes
> documented in docs/design/retired_scripts_patterns.md. Before
> implementing, read:
>
> 1. The "Design principles for continuous processes" section of that
> atlas — every principle is load-bearing. In particular:
> - LLMs for semantic judgment; rules for syntactic validation.
> - Gap-predicate driven, not calendar-driven.
> - Idempotent + version-stamped + observable.
> - No hardcoded entity lists, keyword lists, or canonical-name tables.
> - Three surfaces: FastAPI + orchestra + MCP.
> - Progressive improvement via outcome-feedback loop.
> 2. The theme entry in the atlas matching this task's capability:
> A5 (pick the closest from Atlas A1–A7, Agora AG1–AG5,
> Exchange EX1–EX4, Forge F1–F2, Senate S1–S8, Cross-cutting X1–X2).
> 3. If the theme is not yet rebuilt as a continuous process, follow
> docs/planning/specs/rebuild_theme_template_spec.md to scaffold it
> BEFORE doing the per-instance work.
>
> **Specific scripts named below in this spec are retired and must not
> be rebuilt as one-offs.** Implement (or extend) the corresponding
> continuous process instead.

Task ID: 466d13f2-ec31-44b6-8230-20eb239b6b3a Layer: Atlas Status: Done

Goal

536+ wiki entities had thin infobox_data (only auto-generated fields: name, type,
knowledge_graph_edges, top_relations, associated_diseases). Enrich the 20 most-connected
of these with structured data from the knowledge graph, canonical_entities, wiki_pages,
and the targets table.

Approach

Query knowledge_edges (700K+ edges) to compute per-entity connection counts

Join with wiki_entities to find entities with thin infoboxes (<=5 filled fields)

Sort by connection count descending, pick top 20 unique entities

For each entity, enrich infobox using:

- canonical_entities — aliases, external IDs (UniProt, NCBI, Ensembl), description
- wiki_pages — definition paragraph extraction
- knowledge_edges — associated genes, diseases, drugs, pathways, cell types, interactions, brain regions
- targets — protein name, mechanism, target class (for gene/protein entities)

Merge new data into existing infobox (preserving any existing non-empty values)

Write via db_writes.save_wiki_entity for journaled updates

Enriched Entities

Entity	Type	Connections	Before	After
Genes	index	8142	5	7
cancer	disease	8021	5	11
autophagy	biological_process	7580	5	11
Alzheimer'S Disease	disease	7323	5	10
APOPTOSIS	phenotype	7055	5	6
inflammation	pathway	6960	5	10
Microglia	cell_type	5972	5	10
AGING	phenotype	4818	5	6
TUMOR	disease	4721	5	9
neuroinflammation	biological_process	4676	5	11
CYTOKINES	concept	4349	5	9
mitochondria	organelle	4157	5	8
ASTROCYTES	concept	4155	5	10
NEURODEGENERATIVE DISEASES	concept	4117	5	10
ferroptosis	phenotype	3201	5	7
MITOPHAGY	biological_process	3135	5	10
MITOCHONDRIAL DYSFUNCTION	concept	3048	5	10
neurons	cell_type	2783	5	7
Astrocyte	cell_type	2685	5	10
Erk	protein	2554	5	9

Files

enrichment/enrich_top20_connected_infoboxes.py — enrichment script

Work Log

2026-04-16: Initial investigation. Found all 13,640 wiki_entities already have

infobox_data (auto-generated), but 1,187 have thin data (<=5 filled fields).
The knowledge_edges table has 700K+ edges for computing connection counts.

2026-04-16: Updated THIN_THRESHOLD from 5 to 6 to capture entities with exactly

5 boilerplate fields. Increased scan limit from 500 to 2000 to find 20 thin entities
among the most connected.

2026-04-16: Ran enrichment script successfully. All 20 entities enriched from 5

fields to 6-11 fields each, adding structured data from KG edges, canonical entities,
and wiki page content.

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"
}